frag2bw

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")
#> [1] "/tmp/RtmpQnj5OF/file30f641f53483.bed.bgz.tbi"
# convert to bigwig
frag2bw(bedf, tempfile(fileext=".bw"))
#> Reading in signal...
#> Writing bigwig...