Entering edit mode
hy, I am working with a bamfile, using the package Rsamtools and the function scanBam, some information that are important for me are return as NA, on galaxy and on IGV i can see the information and I don't undersant why.
srq<-scanBam(bamfile1)
srq[["pos"]]
it is given a list of 220134 entries that are all NA, it is the same for qwidth, mapq, cigar, mpos, isize, rname, strand... what is the problem ? thank you
The syntax should be
srq[[1]][["pos"]]
; your command should return NULL. From the help page?scanBam
, does the commandwork as expected? If not, please report the output of
sessionInfo()
, mine isAlso, can you indicate what the position information is likely to be? Is this from a very large genome?