Question: htSeqTools - naming RangedData objects?
7.4 years ago by
Ian Donaldson • 70
Ian Donaldson • 70 wrote:
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 [[alternative HTML version deleted]]
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