diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index cc7f6bc..5cbbe66 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index 75acfbe..2026caf 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 763bd03..00096ff 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 4f321c9..305627f 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index 00e6dd8..4b1fd1e 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index d3fdb3f..e2eeffc 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/creating-a-workflow-step.html b/articles/creating-a-workflow-step.html index 9f2e514..8d3c1cc 100644 --- a/articles/creating-a-workflow-step.html +++ b/articles/creating-a-workflow-step.html @@ -548,7 +548,7 @@

Session info#> [7] grid_4.4.0 bookdown_0.39 fastmap_1.2.0 #> [10] jsonlite_1.8.8 ProtGenerics_1.36.0 BiocManager_1.30.23 #> [13] purrr_1.0.2 fansi_1.0.6 viridisLite_0.4.2 -#> [16] scales_1.3.0 codetools_0.2-20 textshaping_0.3.7 +#> [16] scales_1.3.0 codetools_0.2-20 textshaping_0.4.0 #> [19] jquerylib_0.1.4 cli_3.6.2 rlang_1.1.3 #> [22] Biobase_2.64.0 munsell_0.5.1 withr_3.0.0 #> [25] cachem_1.1.0 yaml_2.3.8 parallel_4.4.0 @@ -560,7 +560,7 @@

Session info#> [43] MASS_7.3-60.2 ragg_1.3.2 pkgconfig_2.0.3 #> [46] desc_1.4.3 pkgdown_2.0.9 pillar_1.9.0 #> [49] bslib_0.7.0 gtable_0.3.5 glue_1.7.0 -#> [52] systemfonts_1.1.0 highr_0.10 xfun_0.44 +#> [52] systemfonts_1.1.0 highr_0.11 xfun_0.44 #> [55] tibble_3.2.1 tidyselect_1.2.1 knitr_1.46 #> [58] farver_2.1.2 htmltools_0.5.8.1 labeling_0.4.3 #> [61] rmarkdown_2.27 signal_1.8-0 compiler_4.4.0 diff --git a/articles/importing-custom-data-formats.html b/articles/importing-custom-data-formats.html index 0c425ab..3b9290f 100644 --- a/articles/importing-custom-data-formats.html +++ b/articles/importing-custom-data-formats.html @@ -88,7 +88,7 @@

Importing custom data formats

Sergio Oller

-

2024-05-23

+

2024-05-30

@@ -313,7 +313,7 @@

Session info [7] grid_4.4.0 bookdown_0.39 fastmap_1.2.0 [10] jsonlite_1.8.8 ProtGenerics_1.36.0 BiocManager_1.30.23 [13] purrr_1.0.2 fansi_1.0.6 viridisLite_0.4.2 -[16] scales_1.3.0 codetools_0.2-20 textshaping_0.3.7 +[16] scales_1.3.0 codetools_0.2-20 textshaping_0.4.0 [19] jquerylib_0.1.4 cli_3.6.2 rlang_1.1.3 [22] Biobase_2.64.0 munsell_0.5.1 withr_3.0.0 [25] cachem_1.1.0 yaml_2.3.8 parallel_4.4.0 @@ -325,7 +325,7 @@

Session info[43] MASS_7.3-60.2 ragg_1.3.2 pkgconfig_2.0.3 [46] desc_1.4.3 pkgdown_2.0.9 bslib_0.7.0 [49] pillar_1.9.0 gtable_0.3.5 glue_1.7.0 -[52] systemfonts_1.1.0 highr_0.10 tidyselect_1.2.1 +[52] systemfonts_1.1.0 highr_0.11 tidyselect_1.2.1 [55] xfun_0.44 tibble_3.2.1 knitr_1.46 [58] farver_2.1.2 htmltools_0.5.8.1 labeling_0.4.3 [61] rmarkdown_2.27 signal_1.8-0 compiler_4.4.0 diff --git a/articles/introduction-to-gcims.html b/articles/introduction-to-gcims.html index aa45753..eeb8797 100644 --- a/articles/introduction-to-gcims.html +++ b/articles/introduction-to-gcims.html @@ -91,7 +91,7 @@

Introduction to GCIMS

GCIMS authors

-

2024-05-23

+

2024-05-30

@@ -292,7 +292,7 @@

Smoothinggeom_line(aes(x = drift_time_ms, y = intensity, colour = Status)) + labs(x = "Drift time (ms)", y = "Intensity (a.u.)"))
-
+
 one_chrom <- getChromatogram(ket1afterfilter, dt_range = 10.4)

 
 one_chrom_smoothed <- smooth(one_chrom, rt_length_s = 3, rt_order = 2)
@@ -305,7 +305,7 @@ 
Smoothinggeom_line(aes(x = retention_time_s, y = intensity, colour = Status)) +
   labs(x = "Retention time (s)", y = "Intensity (a.u.)"))

 

-
You can also apply it to a single sample:

+
You can also apply it to a single sample:

 
 ket1_smoothed <- smooth(
   ket1afterfilter,
@@ -441,13 +441,13 @@ 
Peaks
 #> ℹ Drift time scales: 1, 11, 17, 25, 30
 #> ℹ RIP was detected
 #> • At drift time: [7.533 - 7.933] ms
-#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 63.96 s)

+#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 51.87 s)
 peak_list_ket1 <- peaks(ket1)
 plot_interactive(plot(ket1) +
   overlay_peaklist(peak_list_ket1, color_by = "PeakID"))
-

Then do it on the whole dataset:

+

Then do it on the whole dataset:

 findPeaks(
   dataset,
@@ -469,19 +469,19 @@ 
Peaks
 #> ℹ Drift time scales: 1, 11, 17, 25, 30
 #> ℹ RIP was detected
 #> • At drift time: [7.533 - 7.933] ms
-#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 62.4 s)
+#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 49.53 s)
 #> Using the following scales
 #> ℹ Retention time scales: 1, 26, 39, 59, 64
 #> ℹ Drift time scales: 1, 11, 17, 25, 30
 #> ℹ RIP was detected
 #> • At drift time: [7.533 - 7.933] ms
-#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 63.96 s)
+#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 51.87 s)
 #> Using the following scales
 #> ℹ Retention time scales: 1, 26, 39, 59, 64
 #> ℹ Drift time scales: 1, 11, 17, 25, 30
 #> ℹ RIP was detected
-#> • At drift time: [7.493 - 7.933] ms
-#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 62.4 s)
+#> • At drift time: [7.533 - 7.933] ms +#> • Maximum RIP intensity at: (dt: 7.813 ms, rt: 51.87 s)

You can get any other sample if you like, plot it and plot its peaks on top:

@@ -490,14 +490,14 @@ 
Peaks
 plot_interactive(plot(ket2) +
   overlay_peaklist(peaks(ket2)) )
-

Or plot all the peaks from all the dataset together, overlayed on a +

Or plot all the peaks from all the dataset together, overlayed on a single sample:

 plt <- plot(ket2) +
   overlay_peaklist(peaks(dataset), color_by = "SampleID")
 plot_interactive(plt)
- +

Clustering @@ -519,19 +519,19 @@

Clusteringoverlay_peaklist(peak_list_clustered, color_by = "SampleID") plot_interactive(plt)

-
+
 plt <- plot(ket2) +
   overlay_peaklist(dplyr::filter(peak_list_clustered, !is.na(cluster)), color_by = "cluster")
 plot_interactive(plt)

 

-
The resulting cluster sizes (median position of individual clusters)
+
The resulting cluster sizes (median position of individual clusters)
 is not a good reference for integration. We are working on this.

 
 plt <- plot(ket2) +
   overlay_peaklist(peak_clustering$cluster_stats, color_by = "cluster")
 plot_interactive(plt)

 

-
+

Baseline correction @@ -555,7 +555,7 @@

Baseline correctiongeom_line(aes(x = drift_time_ms, y = Baseline), color = "blue") + labs(x = "Drift time (ms)", y = "Intensity (a.u.)"))

-
+
 one_chrom <- getChromatogram(ket1, dt_range = 10.4)
@@ -645,10 +645,10 @@

Build peak table
 peak_table <- peakTable(peak_list, aggregate_conflicting_peaks = max)
 t(tail(t(peak_table$peak_table_matrix)))
-#>          Cluster22 Cluster19 Cluster25 Cluster18 Cluster06 Cluster07
-#> Ketones1  66.81995  5394.202  123.4277  4712.837        NA        NA
-#> Ketones2 114.77568  5532.655        NA  5225.228  113.5576  101.8653
-#> Ketones3 109.31888  5909.382  174.9371  5482.594  207.6015  111.9301
+#> Cluster10 Cluster22 Cluster17 Cluster18 Cluster03 Cluster01 +#> Ketones1 4721.764 70.1966 5378.463 5222.479 NA NA +#> Ketones2 4739.447 115.7510 5593.831 5336.872 117.1233 100.6062 +#> Ketones3 5031.766 113.9425 5784.134 6197.367 213.2812 106.6575

We showed the last 6 clusters where we have “NA” Values

@@ -659,16 +659,16 @@

Imputationdataset, peak_clustering$cluster_stats) t(tail(t(peak_table_imputed))) -#> Cluster22 Cluster19 Cluster25 Cluster18 Cluster06 Cluster07 -#> Ketones1 66.81995 5394.202 123.42765 4712.837 50.85446 46.61431 -#> Ketones2 114.77568 5532.655 16.50399 5225.228 113.55759 101.86534 -#> Ketones3 109.31888 5909.382 174.93712 5482.594 207.60148 111.93009

+#> Cluster10 Cluster22 Cluster17 Cluster18 Cluster03 Cluster01 +#> Ketones1 4721.764 70.1966 5378.463 5222.479 53.57278 47.57041 +#> Ketones2 4739.447 115.7510 5593.831 5336.872 117.12330 100.60616 +#> Ketones3 5031.766 113.9425 5784.134 6197.367 213.28119 106.65752

As we can see the “NA” values were imputed

 # Implemented until here
 end_time <- Sys.time()
 message("The vignette ran in  ", format(end_time - start_time))
-#> The vignette ran in  1.785006 mins
+#> The vignette ran in 1.802505 mins

Session Info: @@ -707,10 +707,10 @@

Session Info:#> [7] vctrs_0.6.5 tools_4.4.0 generics_0.1.3 #> [10] MassSpecWavelet_1.70.0 stats4_4.4.0 curl_5.2.1 #> [13] parallel_4.4.0 tibble_3.2.1 fansi_1.0.6 -#> [16] highr_0.10 pkgconfig_2.0.3 data.table_1.15.4 +#> [16] highr_0.11 pkgconfig_2.0.3 data.table_1.15.4 #> [19] desc_1.4.3 S4Vectors_0.42.0 lifecycle_1.0.4 #> [22] compiler_4.4.0 farver_2.1.2 stringr_1.5.1 -#> [25] ptw_1.9-16 textshaping_0.3.7 munsell_0.5.1 +#> [25] ptw_1.9-16 textshaping_0.4.0 munsell_0.5.1 #> [28] RcppDE_0.1.7 codetools_0.2-20 htmltools_0.5.8.1 #> [31] snow_0.4-4 sass_0.4.9 lazyeval_0.2.2 #> [34] yaml_2.3.8 plotly_4.10.4 tidyr_1.3.1 diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-28-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-28-1.png index 5c488ed..caa3cc2 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-28-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-28-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-29-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-29-1.png index d462444..a4b4645 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-29-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-29-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-30-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-30-1.png index 3baac71..80b28eb 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-30-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-30-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-31-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-31-1.png index ef5885c..896521f 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-31-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-31-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-43-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-43-1.png index 6859cd7..9847b5e 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-43-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-43-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-46-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-46-1.png index db31d82..38197d7 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-46-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-46-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-48-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-48-1.png index 7abfc65..5e6ee62 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-48-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-48-1.png differ diff --git a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-50-1.png b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-50-1.png index 68174e9..3e32787 100644 Binary files a/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-50-1.png and b/articles/introduction-to-gcims_files/figure-html/unnamed-chunk-50-1.png differ diff --git a/favicon-16x16.png b/favicon-16x16.png index 4e765dc..9ee8a3f 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index a1d70cb..6810a5c 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/pkgdown.yml b/pkgdown.yml index 83b0972..d7d418d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,7 +5,7 @@ articles: creating-a-workflow-step: creating-a-workflow-step.html importing-custom-data-formats: importing-custom-data-formats.html introduction-to-gcims: introduction-to-gcims.html -last_built: 2024-05-23T10:27Z +last_built: 2024-05-30T14:49Z urls: reference: https://sipss.github.io/GCIMS/reference article: https://sipss.github.io/GCIMS/articles diff --git a/reference/GCIMS-generics.html b/reference/GCIMS-generics.html index 7461cdd..6a7a827 100644 --- a/reference/GCIMS-generics.html +++ b/reference/GCIMS-generics.html @@ -81,13 +81,7 @@

GCIMS Generics

align(object, ...) -alignDt(object, ...) - -alignRt_ptw(object, ...) - -alignRt_pow(object, ...) - -alignRt_ip(object, ...) +prealign(object, ...) estimateBaseline(object, ...) @@ -145,15 +139,6 @@

Value

The object, modified

-

The object, modified

- - -

The object, modified

- - -

The object, modified

- -

The object, with a baseline estimated

@@ -176,10 +161,7 @@

Functions

  • filterDt(): Filter in Drift time

  • decimate(): Decimate an object

  • align(): Align an object

    • -

  • alignDt(): Align an object in drift time

    • -

  • alignRt_ptw(): Align an object in retention time

    • -

  • alignRt_pow(): Align an object in retention time

    • -

  • alignRt_ip(): Align an object in retention time

    • +

  • prealign(): Align an object in drift time

  • estimateBaseline(): Estimate the baseline in an object

  • baseline(): Get the baseline of an object

  • baseline(object) <- value: Set the baseline of an object

    • diff --git a/reference/align-GCIMSDataset-method.html b/reference/align-GCIMSDataset-method.html index a270dbb..4176cfe 100644 --- a/reference/align-GCIMSDataset-method.html +++ b/reference/align-GCIMSDataset-method.html @@ -72,7 +72,6 @@

    Align a GCIMS dataset

    align_dt = TRUE, align_ip = TRUE, reference_sample_idx = NULL, - ploynomial_order_ptw = 5, ... )

    @@ -85,7 +84,7 @@

    Arguments

    method_rt

    Method for alignment, should be "ptw" or "pow" -if pow is selected the package "pow must be installed, to do so visit: +if pow is selected the package "pow" must be installed, to do so visit: https://github.com/sipss/pow

    @@ -94,17 +93,13 @@

    Arguments

    align_ip
    -

    if TRUE a multiplicative correction will be done in retention time before applying the other algorithm

    +

    if TRUE a multiplicative correction will be done in retention time before applying the other algorithm

    reference_sample_idx

    One number, the index of the sample to use as reference for the alignment in retention time, if NULL the reference will be calculated automatically depending on the method

    -
    ploynomial_order_ptw
    -

    One number, by default 2, the maximum order of the polynomial for the parametric time warping alignment.

    - -
    ...

    additional parameters for POW alignment

    diff --git a/reference/align-GCIMSSample-method.html b/reference/align-GCIMSSample-method.html index 9103dfd..222daec 100644 --- a/reference/align-GCIMSSample-method.html +++ b/reference/align-GCIMSSample-method.html @@ -1,5 +1,5 @@ -Align a GCIMSSample object, in drift and retention time — align,GCIMSSample-method • GCIMSAlign a GCIMSSample object, in retention time — align,GCIMSSample-method • GCIMS @@ -53,30 +53,18 @@
    -

    Align a GCIMSSample object, in drift and retention time

    +

    Align a GCIMSSample object, in retention time

    -

    Align a GCIMSSample object, in drift and retention time

    +

    Align a GCIMSSample object, in retention time

    # S4 method for GCIMSSample
-align(
-  object,
-  rip_ref_ms,
-  ric_ref,
-  ric_ref_rt,
-  min_start,
-  rt_ref,
-  method_rt,
-  align_dt,
-  align_ip,
-  ploynomial_order_ptw,
-  ...
-)
    +align(object, method_rt, ric_ref, ric_ref_rt, ...)
    @@ -85,8 +73,8 @@

    Arguments

    A GCIMSSample object

    -
    rip_ref_ms
    -

    The reference position of the Reactant Ion Peak in the dataset (in ms)

    +
    method_rt
    +

    Method for alignment, should be "ptw" or "pow"

    ric_ref
    @@ -97,30 +85,6 @@

    Arguments

    The retention times corresponding to ric_ref

    -
    min_start
    -

    minimun injection point, to calculate where to begin the spectrums and cut as few points as posible, to be used in injection point alignment

    - - -
    rt_ref
    -

    retention time reference for alignment to injection point

    - - -
    method_rt
    -

    Method for alignment, should be "ptw" or "pow"

    - - -
    align_dt
    -

    if TRUE, align the drift time axis using a multiplicative correction

    - - -
    align_ip
    -

    if TRUE a multiplicative correction will be done in retention time before applying the other algorithm

    - - -
    ploynomial_order_ptw
    -

    One number, by default 2, the maximum order of the polynomial for the parametric time warping alignment.

    - -
    ...

    Additional arguments passed on to the alignment method.

    diff --git a/reference/alignDt-GCIMSSample-method.html b/reference/alignDt.html similarity index 50% rename from reference/alignDt-GCIMSSample-method.html rename to reference/alignDt.html index 551ef2b..6c7cec3 100644 --- a/reference/alignDt-GCIMSSample-method.html +++ b/reference/alignDt.html @@ -1,5 +1,5 @@ -Align a GCIMSSample in drift time with a multiplicative correction — alignDt,GCIMSSample-method • GCIMSAlign a GCIMSSample in drift time with a multiplicative correction — alignDt • GCIMS @@ -55,7 +55,7 @@

    Align a GCIMSSample in drift time with a multiplicative correction

    - +
    @@ -63,8 +63,7 @@

    Align a GCIMSSample in drift time with a multiplicative correction

    - 
    # S4 method for GCIMSSample
-alignDt(object, rip_ref_ms)
    + 
    alignDt(object, rip_ref_ms)
    diff --git a/reference/alignRt_ip-GCIMSSample-method.html b/reference/alignRt_ip.html similarity index 50% rename from reference/alignRt_ip-GCIMSSample-method.html rename to reference/alignRt_ip.html index b55a46c..f04563a 100644 --- a/reference/alignRt_ip-GCIMSSample-method.html +++ b/reference/alignRt_ip.html @@ -1,5 +1,5 @@ -Align a GCIMSSample in retention time with a multiplicative correction — alignRt_ip,GCIMSSample-method • GCIMSAlign a GCIMSSample in retention time with a multiplicative correction — alignRt_ip • GCIMS @@ -55,7 +55,7 @@

    Align a GCIMSSample in retention time with a multiplicative correction

    - +
    @@ -63,8 +63,7 @@

    Align a GCIMSSample in retention time with a multiplicative correction

    - 
    # S4 method for GCIMSSample
-alignRt_ip(object, min_start, rt_ref)
    + 
    alignRt_ip(object, min_start, rt_ref)
    diff --git a/reference/alignRt_pow-GCIMSSample-method.html b/reference/alignRt_pow.html similarity index 58% rename from reference/alignRt_pow-GCIMSSample-method.html rename to reference/alignRt_pow.html index 0b21c94..117ec8d 100644 --- a/reference/alignRt_pow-GCIMSSample-method.html +++ b/reference/alignRt_pow.html @@ -1,5 +1,5 @@ -Align a GCIMSSample in retention time with parametric optimized warping — alignRt_pow,GCIMSSample-method • GCIMSAlign a GCIMSSample in retention time with parametric optimized warping — alignRt_pow • GCIMS @@ -55,7 +55,7 @@

    Align a GCIMSSample in retention time with parametric optimized warping

    - +
    @@ -63,8 +63,7 @@

    Align a GCIMSSample in retention time with parametric optimized warping

    - 
    # S4 method for GCIMSSample
-alignRt_pow(
+    
    alignRt_pow(
   object,
   ric_ref,
   ric_ref_rt,
diff --git a/reference/alignRt_ptw-GCIMSSample-method.html b/reference/alignRt_ptw-GCIMSSample-method.html
deleted file mode 100644
index 3780b4c..0000000
--- a/reference/alignRt_ptw-GCIMSSample-method.html
+++ /dev/null
@@ -1,120 +0,0 @@
-
-Align a GCIMSSample in retention time using parametric time warping — alignRt_ptw,GCIMSSample-method • GCIMS
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Align a GCIMSSample in retention time using parametric time warping
    
-    
-    
-    
    
-
-    
    
-    
    Align a GCIMSSample in retention time using parametric time warping
    
-    
    
-
-    
    
-    
    # S4 method for GCIMSSample
-alignRt_ptw(object, ric_ref, ric_ref_rt, ploynomial_order_ptw)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    object
    
-
    A GCIMSSample object
    
-
-
-
    ric_ref
    
-
    The reference Reverse Ion Chromatogram
    
-
-
-
    ric_ref_rt
    
-
    The retention times corresponding to ric_ref
    
-
-
-
    ploynomial_order_ptw
    
-
    maximum order of the polynomial to be used
    
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    The modified GCIMSSample
    
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    Developed by Sergio Oller Moreno, Celia Mallafré Muro, Luis Fernandez, Eduardo Caballero Saldivar, Arnau Blanco Borrego, Antonio Pardo Matínez, Santiago Marco Colás.
    
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diff --git a/reference/alignRt_ptw.html b/reference/alignRt_ptw.html
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+Align a GCIMSSample in retention time using parametric time warping — alignRt_ptw • GCIMS
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    Align a GCIMSSample in retention time using parametric time warping
    
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    Align a GCIMSSample in retention time using parametric time warping
    
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    alignRt_ptw(object, ric_ref, ric_ref_rt, ploynomial_order = 5)
    
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    Arguments
    
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    object
    
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    A GCIMSSample object
    
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    ric_ref
    
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    The reference Reverse Ion Chromatogram
    
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    ric_ref_rt
    
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    The retention times corresponding to ric_ref
    
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    ploynomial_order
    
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    maximum order of the polynomial to be used by default 5
    
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    Value
    
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    The modified GCIMSSample
    
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+  
    
+  
+
    
+
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+      
    
+  
    Developed by Sergio Oller Moreno, Celia Mallafré Muro, Luis Fernandez, Eduardo Caballero Saldivar, Arnau Blanco Borrego, Antonio Pardo Matínez, Santiago Marco Colás.
    
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diff --git a/reference/index.html b/reference/index.html
index e67be59..112f0ac 100644
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@@ -69,7 +69,7 @@ 
    All functions 
         
    Create a DelayedOperation object
    
       
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    dtime() getTIS() getRIC() plotTIS() plotRIC() filterDt() decimate() align() alignDt() alignRt_ptw() alignRt_pow() alignRt_ip() estimateBaseline() baseline() `baseline<-`() integratePeaks() 
    
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    dtime() getTIS() getRIC() plotTIS() plotRIC() filterDt() decimate() align() prealign() estimateBaseline() baseline() `baseline<-`() integratePeaks() 
    
         
         
    GCIMS Generics
    
       
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    All functions 
           
    align(<GCIMSSample>) 
    
         
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    Align a GCIMSSample object, in drift and retention time
    
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    Align a GCIMSSample object, in retention time
    
       
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    alignDt(<GCIMSSample>) 
    
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    alignDt() 
    
         
         
    Align a GCIMSSample in drift time with a multiplicative correction
    
       
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    All functions 
         
    Plots to interpret alignment results
    
       
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    alignRt_ip(<GCIMSSample>) 
    
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    alignRt_ip() 
    
         
         
    Align a GCIMSSample in retention time with a multiplicative correction
    
       
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    alignRt_pow(<GCIMSSample>) 
    
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    alignRt_pow() 
    
         
         
    Align a GCIMSSample in retention time with parametric optimized warping
    
       
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    alignRt_ptw(<GCIMSSample>) 
    
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    alignRt_ptw() 
    
         
         
    Align a GCIMSSample in retention time using parametric time warping
    
       
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    All functions plot_interactive() 
    
         
         
    Make a plot interactive
    
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    prealign(<GCIMSSample>) 
    
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    Align a GCIMSSample object, in drift time and to the injection point in retention time
    
       
           
    read_mea() 
    
         
diff --git a/reference/plot_interactive.html b/reference/plot_interactive.html
index 6909a6d..afe9346 100644
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@@ -88,7 +88,7 @@ 
    Examples
    
   ggplot2::geom_point(ggplot2::aes(x = x, y = y))
 plot_interactive(plt)
 
    
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