ssvFetchBamPE.single: fetch a windowed version of a paired-end bam file, returns...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

fetch a windowed version of a paired-end bam file, returns GRanges In contrast to ssvFetchBam, extension of reads to estimated fragment size is not an issue as each read pair represents a fragment of exact size.

Description

fetch a windowed version of a paired-end bam file, returns GRanges In contrast to ssvFetchBam, extension of reads to estimated fragment size is not an issue as each read pair represents a fragment of exact size.

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,
  return_fragSizes = FALSE,
  force_skip_centerFix = 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.
return_fragSizes	boolean. if TRUE returns fragment sizes for all reads per region.
force_skip_centerFix	boolean, if TRUE all query ranges will be used "as is". This is already the case by default if win_method == "summary" but may have applications where win_method == "sample".
...	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.

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.