I am trying to get htSeqTools to create a PCA for my ChIP-seq sample reads.  However, by default there are no labels associated with the sample points in my PCA plot.

METHOD:
I created RangedData objects like this, e.g:
RR05 <- readAligned(dirPath , "RR_20111013_filtered_RR05_bfast_hg18_a3_best_unique_sorted_mapped.bam", type='BAM')

RR05ranges <- RangedData(ranges=IRanges(position(RR05),position(RR05)+width(RR05)), space=chromosome(RR05), strand=strand(RR05))

I have assigned my RangedData to a list like this:
samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges)

Can i assign names like this?
names(samples) <- c("RR05","RR06","RR2_03", "RR2_04")

It works, but my worry is that the order might be different if objects do not have a fixed order.....

Or is there a way of assigning a name to each RangedData object before they are added to a list?

Thank you!  As you can tell i am no expert at using R/Bioconductor!

Ian


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