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Hello,
I am analyzing two MACS2 bed files using ChIPseeker. Individual analysis is OK, but I'm getting an error message for simultaneous analysis of two files when using following ChIPSeeker functions: plotAnnoBar, plotDistToTSS and vennplot. All error messages are similar: Error in XXXX (peakAnnoList) :input object should be a named list (see example below). However, it all works for test files (provided with ChIPseeker) (see example below)
Any advice?
Best regards
Konstantin
> peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, + tssRegion=c(-3000, 3000), verbose=FALSE) > plotAnnoBar(peakAnnoList) Error in plotAnnoBar(peakAnnoList) : input object should be a named list... > plotDistToTSS(peakAnnoList) Error in plotDistToTSS(peakAnnoList) : input object should be a named list... > genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId) > vennplot(genes) Error in vennplot(genes) : input object should be a named list...
> files <- getSampleFiles() > peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, + tssRegion=c(-3000, 3000), verbose=FALSE) > plotAnnoBar(peakAnnoList) > plotDistToTSS(peakAnnoList) > genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId) > vennplot(genes)
Cool, it works now! Thank you very much. Could I suggest to add this into ChIPseeker manual?
Best regards
Konstantin
thanks for the recommendation.
In next release, it will throw warning msg (instead of error) that the input should be a named list and set the named automatically.