Using CAGEr Bioconductor R package

Question

[Waly]

Hi everyone,

I'm trying to use CAGEr offered via Bioconductor https://bioconductor.org/packages/devel/bioc/manuals/CAGEr/man/CAGEr.pdf

I face issues trying to load my .bam files to R, after forging the genome, and defining an index for every file using the samtools; here are more details:

I come to the point where I define sample labels and path, and create a new CAGEset, afterwards I really can't come further, where whenever I try to merge my replicates it shows me this message;

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'rowSums': undefined columns selected

and when I try the getCTSS() function, I get another error;

Error in setnames(CTSS, c("chr", "pos", "strand", sample.label)) : Can't assign 4 names to a 0 column data.table

-- Now again, I'm using several .bam files generated with alignment using Tophat, and converted from sam using the samtools, I don't know why can't CAGEr read/take these files, and how to modify the files for CAGEr to read/accept them, can anybody help?

thanks alot.

Answer 1

[svet]

Did you try with GenomicFiles? Here is what I found: BAM files are (often voluminous) archives of information on short read alignments, and are typically not imported wholesale into R, but left on disk for targeted interrogation or chunk-wise traversal. GenomicFiles is the general class used to manage such collections; Rsamtools defines more specific containers of complementary utility.

Hope it can help.