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

2

Hello: How should I solve this error: ```r 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")) ``` ```r Error in GenomicRangesList(features = feat, flanks = flanks) : could not...

danli349

Error in validObject(.Object) : invalid class "ScoreMatrix" object: superclass "mMatrix" not defined in the environment of the object's class

2

Hello How should I solve this problem? ```r library(genomation) transcriptFile=system.file("extdata", "refseq.hg19.chr20.bed", package="compGenomRData") feat=readTranscriptFeatures(transcriptFile, remove.unusual = TRUE, up.flank = 500, down.flank = 500) prom=feat$promoters # get promoters from the features #...

danli349

> getTargetAnnotationStats(diffAnn,percentage=TRUE,precedence=TRUE) Error in getTargetAnnotationStats(diffAnn, percentage = TRUE, precedence = TRUE) : unused arguments (diffAnn, percentage = TRUE, precedence = TRUE)

Kaustav-93

Hi, I have identified differentially methylated sites with methylKit, and I am interested in annotating the DML/DMR and potentially doing a Gene ontology analysis. I first grabbed all the differentially...

desmodus1984

Hi, I'd like to know what are the defaults for up.flank and down.flank parameters when running readTranscriptFeatures(file.bed) without specifying any parameter ? Thank you very much !

TSolDour

I encountered the readRDS error when installing the package. How could I sove it? ``` > BiocManager::install('genomation') 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement...

Simple53

I am running into an error when running annotateWithFeatures, I have attached the code run and the error. I have verified that the gff file I use matches the file...

maf222