I use a tool called ExomeDepth. 2 months ago I was able to run it and it worked well. Today I decided to analyse different samples and try to count reads:
library(ExomeDepth) data(exons.hg19) bams <- c(long vector of bams) my.counts <- getBamCounts(bed.frame = exons.hg19, bam.files = bams, include.chr = F, referenceFasta = "/path/to/fasta/hg19.fa")
It worked before and it is exactly what is written in the manual: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf . I have R-3.6.1 and ExomeDepth 1.12 (freshly installed).
Error: RangedData objects are deprecated and the rownames setter for RangedData objects is now defunct. Please migrate your code to use GRanges or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData
(obviously the important note says that it is deprecated)
Is there a way to fix it manually or I should wait for the update of the package?
(This is not a crucial thing, I run this tool for benchmarking, so if I won't be able to run it I'll just write it like it is, but if smb has thoughts how to fix it - I'd do this)