I have 6 samples, 3 sets of 2 replicates. Not sure why the error is coming up. Something that seems off is that it says 'computing metrics for 10 samples when I only have 6.
chipObj <- ChIPQC(samples, annotation="hg38")
The error is below.
Checking chromosomes:  "1" Compiling annotation... Computing metrics for 10 samples... list Bam file has 195 contigs Error in sampleQC(bamFile = reads, bedFile = peaks, GeneAnnotation = annotation, : Contigs of interest are not all in Bam file!! In addition: Warning message: In if (is.na(peaks)) peaks = NULL : the condition has length > 1 and only the first element will be used
Let me know if you need any other tests/outputs to help solve this!