grab_seed_frame: grab_seed_frame

In mskilab/loosends: Classifying loose ends in gGraphs

grab_seed_frame

Description

Get reads and their mates overlapping the seed window Designate one member of the pair the "seed" read and the other pair the "mate" read Reverse complement the "mate" read so that the reference frame is the same

Usage

grab_seed_frame(
  reads.dt,
  seed.gr,
  seq.field = "reading.frame",
  forward = TRUE,
  max.n = 0,
  verbose = FALSE
)

Arguments

reads.dt	(data.table) must have columns seqnames, start, end, strand, reading.frame, qname
seed.gr	(GRanges) (stranded) seed window for assembly
seq.field	(character) where is the seq found? default reading.frame
forward	(logical) forward track? if FALSE, will reverse complement the seed frame (default TRUE)
max.n	(numeric) maximum number of low-quality "N" bases (default 0)
verbose	(logical) default FALSE

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.