ssvFetchBamPE.single {seqsetvis}R Documentation

fetch a windowed version of a paired-end bam file, returns GRanges

Description

fetch a windowed version of a paired-end bam file, returns GRanges

Usage

ssvFetchBamPE.single(bam_f, qgr, win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = stats::weighted.mean, anchor = c("left",
  "left_unstranded", "center", "center_unstranded")[3],
  return_data.table = FALSE, max_dupes = Inf, min_isize = 1,
  max_isize = Inf, return_unprocessed = FALSE, ...)

Arguments

bam_f

character or BamFile to load

qgr

GRanges regions to fetchs

win_size

numeric >=1. pileup grabbed every win_size bp for win_method sample. If win_method is summary, this is the number of windows used (confusing, sorry).

win_method

character. one of c("sample", "summary"). Determines if viewGRangesWinSample_dt or viewGRangesWinSummary_dt is used to represent each region in qgr.

summary_FUN

function. only relevant if win_method is "summary". passed to viewGRangesWinSummary_dt.

anchor

character, one of c("center", "center_unstranded", "left", "left_unstranded")

return_data.table

logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE.

max_dupes

numeric >= 1. duplicate reads by strandd start position over this number are removed, Default is Inf.

min_isize

integer. Read pairs must have an isize greater than or equal to this value. Default is 1.

max_isize

integer. Read pairs must have an isize less than or equal to this value. Default is Inf.

return_unprocessed

boolean. if TRUE returns read alignment in data.table. Default is FALSE.

...

passed to Rsamtools::ScanBamParam()

Value

tidy GRanges (or data.table if specified) with pileups from bam file. pileup is calculated only every win_size bp.


[Package seqsetvis version 1.4.0 Index]