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?