Motif Breaker error
0
0
Entering edit mode
@priyankaraina10-14560
Last seen 6.3 years ago

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'

bioconductor motifbreakr plotmb • 821 views
ADD COMMENT

Login before adding your answer.

Traffic: 656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6