I'm using trying to use CSAR (R package, bioconductor) to analyze ChIPseq data. I've read the data in from bam files using Rsamtools and converted it to a data frame. When I run the mappedReads2Nhits function, the object returned seems correct except that for one of my samples the $c1 component is all NA values. The next function in the pipeline throws an error, and returns nothing. I think I've narrowed the problem down to the NAs in $c1, but I don't know how to correct it. Does anyone have experience using this package? --thanks in advance!