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


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.

my.methRaw=processBismarkAln(location ="SRR629540.sorted.sam","SRR629540",assembly="hg19",read.context=c("CpG","CHG","CHH"),save.folder=mySaveFolder)
meth=unite(myobj, destrand=FALSE)

 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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