Error in fragEnds[, 1] : incorrect number of dimensions while using printWigFile function in Basic4Cseq package
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koushik • 0
@koushik-24906
Last seen 3 months ago
United States

Dear All, I am currently using the Basic4Cseq package to analyze my 4C data.. the analysis pipeline seems fine.. I used two "4-based" cutters to generate my library and my goal to generate a wig file to find trans interactions and further downstream analysis.. the following is the pipeline I used

## Bam to Wig using Basic4Cseq
library(Basic4Cseq)

library(BSgenome.Hsapiens.UCSC.hg19)
createVirtualFragmentLibrary(chosenGenome = Hsapiens, firstCutter = "gatc",
                               secondCutter = "ctag", readLength = 75, libraryName = "human_DpnII_Bfal.csv")

library(GenomicAlignments)

## MCF7
libraryFile <- file.path("human_DpnII_Bfal.csv")
bamfile <- file.path("MCF7-DB.bam")
mcf7reads <- readGAlignments(bamfile)  ### path to bam file
mcf7reads


pointsOfInterestFile <- file.path("demo_hg19.bed.txt")
liverPoints<-readPointsOfInterestFile(pointsOfInterestFile)
liverPoints

l3mbtl3Data <- Data4Cseq(viewpointChromosome = "chr11", viewpointInterval = c(61908390, 61908490), 
                         readLength = 75, pointsOfInterest = liverPoints, rawReads = mcf7reads)
l3mbtl3Data

rawFragments(l3mbtl3Data) <- readsToFragments(l3mbtl3Data, libraryFile)
l3mbtl3Data

# normalization of near-cis data
nearCisFragments(l3mbtl3Data) <- normalizeFragmentData(l3mbtl3Data)
head(nearCisFragments(l3mbtl3Data))

getReadDistribution(l3mbtl3Data, useFragEnds = TRUE, outputName = "")
printWigFile(l3mbtl3Data, wigFileName = "MCF7_DB_basic4cseq.wig")

the following report summarise the analysis results:

>getReadDistribution(l3mbtl3Data, useFragEnds = TRUE, outputName = "")
[1] "total reads: 6462494"
[1] "reads on the viewpoint chromosome: 4109392 (63.59% of total reads)"
[1] "reads in the viewpoint region: 3517037 (54.42% of total reads)"
[1] "covered fragment ends in the viewpoint region: 82.7%"

But while implementing

> printWigFile(l3mbtl3Data, wigFileName = "MCF7_DB_basic4cseq.wig")

getting an error Error in fragEnds[, 1] : incorrect number of dimensions

The same pipeline code worked for some other samples with the same format/file type but getting the above error while dealing with others. Can anyone please have any idea how to solve this?

Thank you!

GenomicInteractions Basic4Cseq DNASeq GenomicFiles • 91 views
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