ssvFetchBam.single: fetch a windowed version of a bam file, returns GRanges
In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFetchBam.single

R Documentation

fetch a windowed version of a bam file, returns GRanges

Description

fetch a windowed version of a bam file, returns GRanges

Usage

ssvFetchBam.single(
  bam_f,
  qgr,
  win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = stats::weighted.mean,
  fragLen = NULL,
  target_strand = c("*", "+", "-", "both")[1],
  anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
  return_data.table = FALSE,
  max_dupes = Inf,
  splice_strategy = c("none", "ignore", "add", "only", "splice_count")[1],
  flip_strand = FALSE,
  return_unprocessed = 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`.
`fragLen`	numeric, NULL, or NA. if numeric, supplied value is used. if NULL, value is calculated with fragLen_calcStranded if NA, raw bam pileup with no cross strand shift is returned.
`target_strand`	character. if one of "+" or "-", reads are filtered accordingly. ignored if any other value.
`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.
`splice_strategy`	character, one of c("none", "ignore", "add", "only", "splice_count"). Default is "none" and spliced alignment are asssumed not present. fragLen must be NA for any other value to be valid. "ignore" will not count spliced regions. add" counts spliced regions along with others, "only" will only count spliced regions and ignore others.
`flip_strand`	if TRUE, strand alignment is flipped prior to fragLen extension. Default is FALSE.
`return_unprocessed`	boolean. if TRUE returns read alignment in data.table. Default is FALSE.
`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()