TagMatrixList

[michela12345]

Hi I am wanting to switch from my ChIP-seq analysis to displaying the genes that correspond to the peaks I created with MACS2, these are the commands I was doing so I loaded the reference genome and my data

library(BSgenome.Celegans.UCSC.ce10 ) library(ChIPseeker) txdb <- BSgenome.Celegans.UCSC.ce10 setwd("C:/Users/utente/Desktop/Tesi/Dati") samplefiles <- list.files("C:/Users/utente/Desktop/Tesi/Dati", pattern= ".bed", full.names=T) samplefiles <- as.list(samplefiles) names(samplefiles) <- c("H3K27", "H3K36","H3K4")

promoter <- getPromoters(txdb, upstream=500, downstream=500) tagMatrixList <- lapply(samplefiles, getTagMatrix, windows=promoter)

suppressWarnings(getTagMatrix(samplefiles[[1]], windows=promoter), classes = "warning")

but these are the errors I get that I don't understand how to solve

tagMatrixList <- lapply(samplefiles, getTagMatrix, windows=promoter)

preparing start_site regions by ... 2022-09-21 11:30:52 preparing tag matrix... 2022-09-21 11:30:52 Error in split.default(1:length(windows), as.factor(seqnames(windows))) : group length is 0 but data length > 0 In addition: Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress this warning.) suppressWarnings(getTagMatrix(samplefiles[[1]], windows=promoter), classes = "warning") preparing start_site regions by ... 2022-09-21 11:31:02 preparing tag matrix... 2022-09-21 11:31:02 Error in split.default(1:length(windows), as.factor(seqnames(windows))) : group length is 0 but data length > 0

what can I do? Thank you

[MingLi-929]

The 2 combined objects have no sequence levels in common.

for this warning ,try https://github.com/YuLab-SMU/ChIPseeker/issues/150#issuecomment-1001315578 to see if it can solve.

if this can not solve your problem, it would be convenient to attach your data file to help you.