From 3cb148466ef50e7988616645fef1cd45efc6f2ae Mon Sep 17 00:00:00 2001 From: Daniel Gatti Date: Wed, 9 Aug 2017 12:52:23 -0400 Subject: [PATCH] Changed directory name & added cecum qtl mapping loop --- cecum_lipids_JAX_loop.sh | 12 ++++++ gather_qtl_output.sh | 50 ++++++++++++------------- harvest_max_qtl.sh | 34 ++++++++--------- harvest_thr_qtl.sh | 34 ++++++++--------- liver_lipids_JAX_coef_assoc_loop.sh | 10 ++--- liver_lipids_JAX_loop.sh | 6 +-- liver_lipids_UWisc_loop.sh | 6 +-- liver_metabolites_JAX_loop.sh | 6 +-- liver_metabolites_JAX_sex_gen_loop.sh | 6 +-- liver_metabolites_UWisc_loop.sh | 6 +-- liver_metabolites_UWisc_loop_sex_gen.sh | 6 +-- plasma_lipids_UWisc_loop.sh | 6 +-- qtl2_coef_assoc_engine.sh | 2 +- qtl2_scan_engine.sh | 2 +- qtl_heatmap.sh | 50 ++++++++++++------------- qtl_histogram.sh | 4 +- 16 files changed, 126 insertions(+), 114 deletions(-) create mode 100644 cecum_lipids_JAX_loop.sh diff --git a/cecum_lipids_JAX_loop.sh b/cecum_lipids_JAX_loop.sh new file mode 100644 index 0000000..dc02e28 --- /dev/null +++ b/cecum_lipids_JAX_loop.sh @@ -0,0 +1,12 @@ +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts + +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_cecum_lipids_qtl2_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Cecum/lipids_norm_jax/ +SIZE=20 + +# Set the maximum number in the loop to ceiling(MAXCOL/SIZE). +for i in {1..113} +do + qsub -v INDIR=${INPUT},OUTPREFIX=${OUTPUT},CHUNKSIZE=${SIZE},CHUNKNUM=${i} qtl2_scan_engine.sh + sleep 30s +done diff --git a/gather_qtl_output.sh b/gather_qtl_output.sh index b11f7b9..37d55d8 100644 --- a/gather_qtl_output.sh +++ b/gather_qtl_output.sh @@ -4,60 +4,60 @@ module load R/3.3.2 # For each chromosome, harvest the maximum peak per analyte. -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_jax.Rout # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_jax_sex_gen.Rout # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_uwisc.Rout # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_metabolites_uwisc_sex_gen.Rout # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_jax/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_lipids_jax.Rout # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_liver_lipids_uwisc.Rout # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_jax/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_plasma_lipids_jax.Rout # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/ -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm -FIGDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/ +INPUTDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/ +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm +FIGDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/ R --no-save --args ${INPUTDIR} ${OUTPUTPREFIX} ${FIGDIR} < gather_qtl_output.R > gather_qtl_plasma_lipids_uwisc.Rout diff --git a/harvest_max_qtl.sh b/harvest_max_qtl.sh index 04e91a8..b04d136 100644 --- a/harvest_max_qtl.sh +++ b/harvest_max_qtl.sh @@ -4,56 +4,56 @@ module load R/3.3.2 # For each chromosome, harvest the maximum peak per analyte. -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts # Arguments. # INPUTFILE: full path to aggregated QTL LOD file (as *.rds). # OUTPUTPREFIX: full path to output file prefix. We append .csv and .rds to it. # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_jax.Rout # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_jax_sex_gen.Rout # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_uwisc.Rout # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_metabolites_uwisc_sex_gen.Rout # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_lipids_jax.Rout # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_liver_lipids_uwisc.Rout # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_plasma_lipids_jax.Rout # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} < harvest_max_qtl.R > harvest_QTL_plasma_lipids_uwisc.Rout diff --git a/harvest_thr_qtl.sh b/harvest_thr_qtl.sh index dbc7e74..1330a88 100644 --- a/harvest_thr_qtl.sh +++ b/harvest_thr_qtl.sh @@ -5,54 +5,54 @@ module load R/3.3.2 # For each chromosome, harvest the maximum peak above a given threshold for each analyte. # Run this AFTER the harvest_max_qtl.R script because it creates the aggregated QTL file. -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts THR=6 # JAX normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_jax.Rout # JAX normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_jax_sex_gen.Rout # U. Wisc. normalized liver metabolites. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_uwisc.Rout # U. Wisc. normalized liver metabolites with sex & gen as covariates. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_metabolites_uwisc_sex_gen.Rout # JAX normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_lipids_jax.Rout # U. Wisc. normalized liver lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_liver_lipids_uwisc.Rout # JAX normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_plasma_lipids_jax.Rout # U. Wisc. normalized plasma lipids. (NOTE: Place a / at the end of the paths) -INPUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds -OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm +INPUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds +OUTPUTPREFIX=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm R --no-save --args ${INPUTFILE} ${OUTPUTPREFIX} ${THR} < harvest_thr_qtl.R > harvest_qtl_plasma_lipids_uwisc.Rout diff --git a/liver_lipids_JAX_coef_assoc_loop.sh b/liver_lipids_JAX_coef_assoc_loop.sh index d07b20b..39f9157 100644 --- a/liver_lipids_JAX_coef_assoc_loop.sh +++ b/liver_lipids_JAX_coef_assoc_loop.sh @@ -1,13 +1,13 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts # The full path to the qtl2 data input file. -DF=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata +DF=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata # The full path to the QTL summary file. -QF=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_qtl_summary_thresh_6.csv +QF=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_qtl_summary_thresh_6.csv # Output directory for data. -OD=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/ +OD=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/ # Output directory for figures. -FD=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/Liver/lipids_norm_jax/ +FD=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/Liver/lipids_norm_jax/ # Number of analytes to map in one chunk. SIZE=20 diff --git a/liver_lipids_JAX_loop.sh b/liver_lipids_JAX_loop.sh index cdb8552..07d2316 100644 --- a/liver_lipids_JAX_loop.sh +++ b/liver_lipids_JAX_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/liver_lipids_UWisc_loop.sh b/liver_lipids_UWisc_loop.sh index 59fd3e4..b725344 100644 --- a/liver_lipids_UWisc_loop.sh +++ b/liver_lipids_UWisc_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_UWisc_input.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_lipids_qtl2_UWisc_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/liver_metabolites_JAX_loop.sh b/liver_metabolites_JAX_loop.sh index 36491f7..9fae4d4 100644 --- a/liver_metabolites_JAX_loop.sh +++ b/liver_metabolites_JAX_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_metabolites_qtl2_input.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_metabolites_qtl2_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/liver_metabolites_JAX_sex_gen_loop.sh b/liver_metabolites_JAX_sex_gen_loop.sh index 3e47b3e..f6b1f83 100644 --- a/liver_metabolites_JAX_sex_gen_loop.sh +++ b/liver_metabolites_JAX_sex_gen_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_metabolites_qtl2_input_sex_gen.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_metabolites_qtl2_input_sex_gen.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/liver_metabolites_UWisc_loop.sh b/liver_metabolites_UWisc_loop.sh index a4b3a88..8eb9a99 100644 --- a/liver_metabolites_UWisc_loop.sh +++ b/liver_metabolites_UWisc_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_metabolites_UWisc_qtl2_input.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_metabolites_UWisc_qtl2_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/liver_metabolites_UWisc_loop_sex_gen.sh b/liver_metabolites_UWisc_loop_sex_gen.sh index 06bb698..4f61c9a 100644 --- a/liver_metabolites_UWisc_loop_sex_gen.sh +++ b/liver_metabolites_UWisc_loop_sex_gen.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_liver_metabolites_UWisc_qtl2_input_sex_gen.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_liver_metabolites_UWisc_qtl2_input_sex_gen.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/plasma_lipids_UWisc_loop.sh b/plasma_lipids_UWisc_loop.sh index 1d2f31e..4f9ac2c 100644 --- a/plasma_lipids_UWisc_loop.sh +++ b/plasma_lipids_UWisc_loop.sh @@ -1,7 +1,7 @@ -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts -INPUT=/hpcdata/gac/derived/Attie_DO_Liver_Metabolomics/qtl2_input/attie_plasma_lipids_qtl2_UWisc_input.Rdata -OUTPUT=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/ +INPUT=/hpcdata/gac/derived/Attie_DO_Metabolomics/qtl2_input/attie_plasma_lipids_qtl2_UWisc_input.Rdata +OUTPUT=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/ SIZE=20 # Set the maximum number in the loop to ceiling(MAXCOL/SIZE). diff --git a/qtl2_coef_assoc_engine.sh b/qtl2_coef_assoc_engine.sh index 78b78c0..c22a91a 100644 --- a/qtl2_coef_assoc_engine.sh +++ b/qtl2_coef_assoc_engine.sh @@ -1,7 +1,7 @@ #!/bin/bash -l #PBS -q short -l nodes=1:ppn=1,walltime=3:59:00 module load R/3.3.2 -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts # DF: The full path to the qtl2 data input file. # QF: The full path to the QTL summary file. diff --git a/qtl2_scan_engine.sh b/qtl2_scan_engine.sh index 57e2bae..8d0e4a7 100644 --- a/qtl2_scan_engine.sh +++ b/qtl2_scan_engine.sh @@ -1,6 +1,6 @@ #!/bin/bash -l #PBS -q short -l nodes=1:ppn=1,walltime=2:00:00 module load R/3.3.2 -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts R --no-save --args $INDIR $OUTPREFIX $CHUNKSIZE $CHUNKNUM $MAXCOL < qtl2_scan_engine.R > qtl2_scan_engine_${CHUNKNUM}.Rout diff --git a/qtl_heatmap.sh b/qtl_heatmap.sh index fd74387..386067f 100644 --- a/qtl_heatmap.sh +++ b/qtl_heatmap.sh @@ -1,6 +1,6 @@ #!/bin/bash -l #PBS -q short -l nodes=1:ppn=1,walltime=3:59:00 -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts module load R/3.3.2 @@ -13,86 +13,86 @@ LODTHR=8 ########## # Liver lipids, JAX normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_jax/liver_lipids_jax_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/liver_lipids_jax_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_lipids_jax_norm.Rout ########## # Known liver lipids, JAX normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl_known_only.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_jax/known_liver_lipids_jax_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_jax/liver_lipids_jax_norm_all_qtl_known_only.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_jax/known_liver_lipids_jax_qtl_heatmap.png LODTHR=8 R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_liver_lipids_jax_norm.Rout ########## # Liver lipids, U. Wisc. normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/liver_lipids_uwisc_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/liver_lipids_uwisc_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_lipids_uwisc_norm.Rout ########## # Known liver lipids, U. Wisc. normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl_known_only.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/known_liver_lipids_uwisc_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/lipids_norm_uwisc/liver_lipids_uwisc_norm_all_qtl_known_only.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_lipids_norm_uwisc/known_liver_lipids_uwisc_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_liver_lipids_uwisc_norm.Rout ########## # Liver metabolites, JAX normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax/liver_metabolites_jax_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax/liver_metabolites_jax_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax/liver_metabolites_jax_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_jax_norm.Rout ########## # Liver metabolites, JAX normalized, sex & gen. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/liver_metabolites_jax_sex_gen_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_jax_sex_gen/liver_metabolites_jax_norm_sex_gen_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_jax_sex_gen/liver_metabolites_jax_sex_gen_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_sex_gen_jax_norm.Rout ########## # Liver metabolites, U. Wisc. normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/liver_metabolites_uwisc_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc/liver_metabolites_uwisc_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc/liver_metabolites_uwisc_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_uwisc_norm.Rout ########## # Liver metabolites, U. Wisc. normalized, sex & gen. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_sex_gen_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Liver/metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_norm_sex_gen_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/liver_metabolites_norm_uwisc_sex_gen/liver_metabolites_uwisc_sex_gen_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_liver_metabolites_uwisc_sex_gen_norm.Rout ########## # Plasma lipids, JAX normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_jax/plasma_lipids_jax_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/plasma_lipids_jax_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_lipids_jax_norm.Rout ########## # Known plasma lipids, JAX normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl_known_only.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_jax/known_plasma_lipids_jax_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_jax/plasma_lipids_jax_norm_all_qtl_known_only.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_jax/known_plasma_lipids_jax_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_plasma_lipids_jax_norm.Rout ########## # Plasma lipids, U. Wisc. normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/plasma_lipids_uwisc_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/plasma_lipids_uwisc_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_plasma_lipids_uwisc_norm.Rout ########## # Known plasma lipids, U. Wisc. normalized, sex, gen & batch. -INFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl_known_only.rds -OUTFILE=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/known_plasma_lipids_uwisc_qtl_heatmap.png +INFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/QTL/Plasma/lipids_norm_uwisc/plasma_lipids_uwisc_norm_all_qtl_known_only.rds +OUTFILE=/hpcdata/gac/projects/Attie_DO_Metabolomics/figures/QTL/plasma_lipids_norm_uwisc/known_plasma_lipids_uwisc_qtl_heatmap.png R --no-save --args ${INFILE} ${OUTFILE} ${LODTHR} < qtl_heatmap.R > qtl_heatmap_known_plasma_lipids_uwisc_norm.Rout diff --git a/qtl_histogram.sh b/qtl_histogram.sh index 7f97c93..90f6c92 100644 --- a/qtl_histogram.sh +++ b/qtl_histogram.sh @@ -6,8 +6,8 @@ module load R/3.3.2 # output.file: full path to the output figure file as a PNG. # thr: LOD threshold to use when selecting QTL peaks. -cd /hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/scripts -BASEDIR=/hpcdata/gac/projects/Attie_DO_Liver_Metabolomics/ +cd /hpcdata/gac/projects/Attie_DO_Metabolomics/scripts +BASEDIR=/hpcdata/gac/projects/Attie_DO_Metabolomics/ ########## # Liver lipids: JAX: sex, gen & batch