Question: Some questions for the 'readTranscriptFeatures' function of the R package-"genomation" when I doing RRBS analysis
0
gravatar for ying.senhong
6 weeks ago by
ying.senhong0 wrote:

Hello,

When I was doing the RRBS analysis, I used bismark+methylKit. After find DMR, I try to annotation these DMRs. But when I using the 'readTranscriptFeatures' function of the R package-"genomation" and get some errors when I read this gene annotation information as the following context.

mySaveFolder="G:/Methylation/bismark_test/methylKit_analysis"
my.methRaw=processBismarkAln(location="SRR629538.sorted.sam",sample.id="SRR629538",assembly="hg19",read.context=c("CpG","CHG","CHH"),save.folder=mySaveFolder)
my.methRaw=processBismarkAln(location ="SRR629540.sorted.sam",sample.id="SRR629540",assembly="hg19",read.context=c("CpG","CHG","CHH"),save.folder=mySaveFolder)
myobj=methRead(list("SRR629538_CpG.txt","SRR629540_CpG.txt"),sample.id=list("SRR629538","SRR629540"),assembly="hg19",treatment=c(1,0),context="CpG")
meth=unite(myobj, destrand=FALSE)
myDiff=calculateDiffMeth(meth,num.cores=12)
myDiff25p=getMethylDiff(myDiff,difference=25,qvalue=0.01)
library(genomation)
gene.obj=readTranscriptFeatures("hg19_refseq_gencodev19.bed")




 Reading the table...
    Calculating intron coordinates...
    Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
      solving row 8835: negative widths are not allowed
    In addition: Warning message:
    In cbind(...) :
      number of rows of result is not a multiple of vector length (arg 1)

Can anyone guide how to solve this error?

R • 115 views
ADD COMMENTlink modified 6 weeks ago by ATpoint15k • written 6 weeks ago by ying.senhong0

Please use the formatting bar to indicate code and error messages.

enter image description here

ADD REPLYlink written 6 weeks ago by ATpoint15k

well, can you look at row 8835 and make sure end>=start?

ADD REPLYlink written 6 weeks ago by Jeremy Leipzig18k
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