Dear all,
I was running MEDIPS. I use the following command lines. But error occurs, which is showed below. I really appreciate it if someone can help me to solve it. Thanks.
library(MEDIPS)
bam.file.HIV.Rep1.MeDIP = "Jurkat_HIV.sort.rmdup.bam"
bam.file.HIV.Rep1.MeDIP = "Jurkat_HIV.sort.rmdup.bam"
library(BSgenome.Hsapiens.UCSC.hg38)
HIV_MeDIP = MEDIPS.createSet(file=bam.file.HIV.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg38", uniq=1e-3, extend=300, shift=0, window_size=100)
HIV5aza_MeDIP = MEDIPS.createSet(file=bam.file.HIV5aza.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg38", uniq=1e-3, extend=300, shift=0, window_size=100)
CS = MEDIPS.couplingVector(pattern="CG", refObj=HIV5aza_MeDIP)
mr.edgeR = MEDIPS.meth(MSet1=HIV_MeDIP, MSet2=HIV5aza_MeDIP, CSet=CS, p.adj="holm", diff.method="edgeR", MeDIP="F", CNV=F, minRowSum=10)
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Preprocessing MEDIPS SET 1 in MSet1...
Preprocessing MEDIPS SET 1 in MSet2...
Differential coverage analysis...
Extracting count windows with at least 10 reads...
Execute edgeR for count data of 0 windows...
(Neglecting parameter 'type')
Creating a DGEList object...
Apply trimmed mean of M-values (TMM) for library sizes normalization...
There is no replication, setting dispersion to bcv^2 where bcv=0.01.
Please consider http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf section 2.9.
Calculating differential coverage...
*Error in rownames<-(*tmp*, value = c("tag.1", "tag.0")) :
length of 'dimnames' [1] not equal to array extent
In addition: Warning message: In edgeR::DGEList(counts = values[filter, ], group = edRObj.group) : Zero library size detected.*