I did a whole series of alignments of bam files to my genome using tools in the following R libraries in Bioconductor
library(GenomicRanges) library(rtracklayer) library(Rsamtools) library(limma) library(GenomicAlignments)
I used the following commands to create coverage vectors:
Cov_1 <- coverage(alignGR_1) smoothed the vectors and plotted them out.: plot(smoothCov_1_a, col="red", type="l", ylab="Number of reads", xlab="bp from range start")
All worked well.
I exported the coverage vectors so that I could analyse them with respect to sequence features but when I look inside them I did not find numbers but unicode characters. Seems like a silly mistake but I am lost as to what it might be?