`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

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[danli349]

@al2na

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