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Question: Motif Breaker error
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gravatar for priyankaraina10
6 days ago by
priyankaraina100 wrote:

Hi 

I am running motif breaker script on my data

I am using the following script:

library(motifbreakR)
library(MotifDb)
library(BSgenome)
library(BSgenome.Hsapiens.UCSC.hg19)
library(SNPlocs.Hsapiens.dbSNP142.GRCh37)
data(motifbreakR_motif)
data(homer)

print("load file")
snps.mb.frombed <- snps.from.file(file="ptf1a_snps.bed",search.genome=BSgenome.Hsapiens.UCSC.hg19, format="bed")
print("file loaded")

print("homer analysis")
snps_homer<-motifbreakR(snpList=snps.mb.frombed, filterp=TRUE, pwmList=homer, threshold=1e-4, method="ic", bkg=c(A=0.25, C=0.25, G=0.25, T=0.25),BPPARAM=BiocParallel::SerialParam())
write.table(as.data.frame(snps_homer,row.names=NULL),file="snps.bed.homer.txt",sep="\t",quote=FALSE)
plotMB(results = snps_homer, rsid = "chr10:23508446:A:C", effect = "strong")

 

However at step:

plotMB(results = snps_homer, rsid = "chr10:23508446:A:C", effect = "strong")

I get the following error:

Warning messages:
1: running command 'gswin32c.exe -q -dBATCH -dNOPAUSE -sDEVICE=ps2write -sOutputFile=C:\Users\Priyanka\AppData\Local\Temp\RtmpI7h96k\file1980721e17b2 -sstdout=C:\Users\Priyanka\AppData\Local\Temp\RtmpI7h96k/stack.ps.xml capturestack.ps' had status 127 
2: In .local(GdObject, ...) :
  There have been errors in the detail plotting function:
Error in PostScriptTrace(ps.file, paste0(ps.file, ".xml")) : 
  status 127 in running command 'gswin32c.exe -q -dBATCH -dNOPAUSE -sDEVICE=ps2write -sOutputFile=C:\Users\Priyanka\AppData\Local\Temp\RtmpI7h96k\file1980721e17b2 -sstdout=C:\Users\Priyanka\AppData\Local\Temp\RtmpI7h96k/stack.ps.xml capturestack.ps'

ADD COMMENTlink written 6 days ago by priyankaraina100
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