frag2bw: frag2bw

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

frag2bw

Description

Creates a coverage bigwig file from a Tabix-indexed fragment file.

Usage

frag2bw(
  tabixFile,
  output_bw,
  paired = TRUE,
  binWidth = 20L,
  extend = 0L,
  scaling = TRUE,
  type = c("full", "center", "start", "end", "ends"),
  barcodes = NULL,
  strand = c("*", "+", "-"),
  shift = 0L,
  log1p = FALSE,
  exclude = NULL,
  minFragLength = 1L,
  maxFragLength = 5000L,
  keepSeqLvls = NULL,
  useScore = FALSE,
  forceSeqlevelsStyle = NULL,
  only = NULL,
  format = "bed",
  binSummarization = c("max", "min", "mean"),
  verbose = TRUE
)

Arguments

tabixFile	The path to a tabix-indexed bam file, or a TabixFile object.
output_bw	The path to the output bigwig file
paired	Logical; whether the coordinates are that of fragments, as opposed to single-end reads where the only one end of the fragments is given. TRUE by default.
binWidth	The window size. A lower value (min 1) means a higher resolution, but larger file size.
scaling	Either TRUE (performs Count Per Million scaling), FALSE (no scaling), or a numeric value by which the signal will be divided. If 'bgbam' is given and 'scaling=TRUE', the background will be scaled to the main signal.
type	Type of the coverage to compile. Either full (full read/fragment), start (count read/fragment start locations), end, center, or 'ends' (both ends of the read/fragment).
barcodes	An optional list of barcodes to use (assuming that the file contains the column)
strand	Strand(s) to capture (any by default).
shift	Shift (from 3' to 5') by which reads/fragments will be shifted. If 'shift' is an integer vector of length 2, the first value will represent the shift for the positive strand, and the second for the negative strand.
exclude	An optional GRanges of regions for which overlapping reads should be excluded.
minFragLength	Minimum fragment length (ignored if 'paired=FALSE')
maxFragLength	Maximum fragment length (ignored if 'paired=FALSE')
keepSeqLvls	An optional vector of seqLevels (i.e. chromosomes) to include.
useScore	Whether to use the score column (if any) as coverage weights.
forceSeqlevelsStyle	If specified, forces the use of the specified seqlevel style for the output bigwig. Can take any value accepted by 'seqlevelsStyle'.
only	An optional GRanges of regions for which overlapping reads should be included. If set, all other reads are discarded.
format	The format of the fragment file.
binSummarization	The method to summarize nucleotides into each bin, either "max" (default), "min" or "mean".
verbose	Logical; whether to print progress messages

Value

The bigwig filepath. Alternatively, if 'output_bw=NA_character_', the coverage data is not written to file but returned.

Examples

# we first create a fake tabix file:
library(GenomicRanges)
library(rtracklayer)
reads <- GRanges(rep(c("1","2"), c(5,2)),
                 IRanges(5000+10*1:7, width=100))
bedf <- tempfile(fileext=".bed")
rtracklayer::export.bed(reads, bedf)
bedf <- Rsamtools::bgzip(bedf)
Rsamtools::indexTabix(bedf, format="bed")
# convert to bigwig
frag2bw(bedf, tempfile(fileext=".bw"))

ETHZ-INS/epiwraps documentation built on Oct. 27, 2024, 8:02 p.m.