Question: Some questions for the 'readTranscriptFeatures' function of the R package-"genomation" when I doing RRBS analysis
0
gravatar for ying.senhong
10 months 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 • 419 views
ADD COMMENTlink modified 10 months ago by ATpoint28k • written 10 months ago by ying.senhong0
1

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

ADD REPLYlink written 10 months ago by Jeremy Leipzig18k

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

enter image description here

ADD REPLYlink written 10 months ago by ATpoint28k
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