Subsetting data from BAM file using R tools

Question

[Ilya IN]

Good day to all! This is my first post in Biostars.

I have BAM file with Paired-End RNA seq reads, and I need filter this file by "isize" field: extract the reads with isize not equal to NA and with absolute value of isize lower than treshold (in this case, 642 bp). After all, I must write this subset into SAM file (because this type is required for package which I will use).

I tried use R package Rsamtools for this, but my experience in R is inadequate for solve this problem quickly. If I'm right, settings "param" of function filterBam() can help (if I get BAM file with targer subset, I'll use asSam() to convert into SAM format). Remove reads with isize == NA is possible by means scanBamFlag:

flag <- scanBamFlag(isPaired = TRUE, hasUnmappedMate = FALSE)

But I have no idea about filtration by treshold (abs(bamFile$isize) <= 642). How I can do it in R?

Thanks in advance for your help!

Answer 1

[karimse07]

you can use pmax function in R for athreshold

[Sukhi Singh]

I don't see pmax working in this case!

[Ilya IN]

Thank you for answer, but how it can help me with BAM file subsetting? Can you give an example?