Error in GenomicRangesList(features = feat, flanks = flanks) : could not find function "GenomicRangesList"

[danli349]

Hello:

How should I solve this error:

library(GenomicRanges)
library(genomation)
cpg.file=system.file("extdata", "cpgi.hg18.bed.txt", 
                                        package = "methylKit")
cpg.obj=readFeatureFlank(cpg.file,
                           feature.flank.name=c("CpGi","shores"))

Error in GenomicRangesList(features = feat, flanks = flanks) :
could not find function "GenomicRangesList"

Thanks a lot

[al2na]

this is probably something should be fixed on our end. GenomicRanges might have changed function names etc, will look into it. you can probably get the same functionality from a couple of lines of code in GenomicRanges

…

On Wed, Mar 6, 2024 at 9:25 PM Dan Li ***@***.***> wrote: Hello: How should I solve this error: library(GenomicRanges) library(genomation)cpg.file=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit")cpg.obj=readFeatureFlank(cpg.file, feature.flank.name=c("CpGi","shores")) Error in GenomicRangesList(features = feat, flanks = flanks) :could not find function "GenomicRangesList" Thanks a lot — Reply to this email directly, view it on GitHub <#211>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE32EOEEI4VCC6QZDTJ2O3YW53T5AVCNFSM6AAAAABEJXPAQ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3TEMZWGYZTMNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[danli349]

@al2na

I used genomation_1.19.1 and GenomicRanges_1.54.1, should I change to an old version of GenomicRanges?