Hi. I'm trying to analyze a CAGE-seq data using CAGEr but I can not get pass the getCTSS command.
The input is 8 single-end bam files (<210Mb). They are the result of mapping against Arabidopsis genome from TAIR10.
Following the package vignette the data was loaded using,
my.inputFiles <- list.files(bam.dir, pattern = "*.bam", recursive = TRUE, full.names = TRUE) my.genome <- "BSgenome.Athaliana.TAIR.TAIR9" ce <- CAGEexp( genomeName = my.genome , inputFiles = my.inputFiles , inputFilesType = "bam" , sampleLabels = gsub(".bam", "", basename(my.inputFiles)) )
But when I ran getCTSS I got the following errors (Different versions of the command were tested)
> getCTSS(ce, correctSystematicG = FALSE) Error in checkSlotAssignment(object, name, value) : assignment of an object of class “IRanges” is not valid for slot ‘ranges’ in an object of class “UnstitchedGPos”; is(value, "UnstitchedIPos") is not TRUE > getCTSS(ce, correctSystematicG = FALSE, removeFirstG = FALSE) Error in .try_to_coerce_to_GRanges_first(from, "UnstitchedGPos") : object to coerce to UnstitchedGPos couldn't be coerced to GRanges first
Thank you in advance for your help...