You should use scanBam function from RSamtools along with GenomicRanges

E.g

what <- c("rname", "strand", "pos", "seq", "qual", "maps")
param <- ScanBamParam(what = what, flag = scanBamFlag(isUnmappedQuery = FALSE))
bam <- scanBam(bam.file, param = param)

Then use GRanges to filter for specific coordinates.

First create an object with the above command and execute with system

Ex:

x="samtools view -bS -F 4 sorted_file.bam transcript_xx > transcript_xx.bam"
system(x)