bam2bw: bam2bw: create a coverage bigwig file from an alignment bam...

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

bam2bw: create a coverage bigwig file from an alignment bam file.

Description

bam2bw: create a coverage bigwig file from an alignment bam file.

Usage

bam2bw(
  bamfile,
  output_bw,
  bgbam = NULL,
  paired = NULL,
  binWidth = 20L,
  extend = 0L,
  scaling = TRUE,
  shift = 0L,
  type = c("full", "center", "start", "end", "ends"),
  compType = c("log2ratio", "subtract", "log10ppois", "log10FE"),
  strand = c("*", "+", "-"),
  strandMode = 1,
  log1p = FALSE,
  exclude = NULL,
  includeDuplicates = TRUE,
  includeSecondary = FALSE,
  minMapq = 1L,
  minFragLength = 1L,
  maxFragLength = 5000L,
  keepSeqLvls = NULL,
  splitByChr = 3,
  pseudocount = 1L,
  localBackground = 1L,
  only = NULL,
  zeroCap = TRUE,
  forceSeqlevelsStyle = NULL,
  verbose = TRUE,
  binSummarization = c("mean", "max", "min"),
  ...
)

Arguments

bamfile	The path to the signal bam file.
output_bw	The path to the output bigwig file
bgbam	The optional path to the control/input bam file to compute relative signal (see the 'compType' argument).
paired	Logical; whether to consider fragments instead of reads for paired-end data. For spliced (e.g. RNA-seq) data, paired should always be set to FALSE.
binWidth	The window size. A lower value (min 1) means a higher resolution, but larger file size.
extend	The amount *by* which to extend single-end reads (e.g. fragment length minus read length). If 'paired=TRUE' and 'type' is either 'ends' or 'center', then the extension will be applied after taking the (shifted) fragment ends or centers, resulting in ranges of width equal to 'extend'.
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.
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. For ATACseq data, one normally uses 'shift=c(4L,-5L)'.
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).
compType	The type of relative signal to compute (ignored if 'bgbam' isn't given). Can either be 'log2ratio' (log2-foldchange between signals), 'subtract' (difference), 'log10ppois' (rounded -log10 poisson p-value), 'log10FE' (log10 fold-enrichment). For fold-based signals, 'pseudocount' will be added before computing the ratio. By default negative values are capped (see 'zeroCap').
strand	Strand(s) to capture (any by default).
strandMode	The strandMode of the data (whether the strand is given by the first or second mate, which depends on the library prep protocol). See strandMode for more information. This parameter has no effect unless one of the 'strand', 'extend' parameters or a strand-specific 'shift' are used.
log1p	Whether to log-transform ('log(x+1)') the (scaled) signal. Ignored when the signal is relative to a background.
exclude	An optional GRanges of regions for which overlapping reads should be excluded.
includeDuplicates	Logical, whether to include reads flagged as duplicates.
includeSecondary	Logical; whether to include secondary alignments
minMapq	Minimum mapping quality (1 to 255)
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.
splitByChr	Whether to process chromosomes separately, and if so by how many chunks. The should not affect the output, and is simply slightly slower and consumes less memory. Can be a logical value (in which case each chromosome is processed separately), but we instead recommend giving a positive integer indicating the number of chunks.
pseudocount	The count to be added before fold-enrichment calculation between signals. Ignored if 'compType="subtract"'.
localBackground	A (vector of) number of windows around each tile/position for which a local background will be calculated. The background used will be the maximum of the one at the given position or of the mean of each of the local backgrounds.
only	An optional GRanges of regions for which overlapping reads should be included. If set, all other reads are discarded.
zeroCap	Logical; whether to cap values below zero to zero when producing relative signals.
forceSeqlevelsStyle	If specified, forces the use of the specified seqlevel style for the output bigwig. Can take any value accepted by 'seqlevelsStyle'.
verbose	Logical; whether to print progress messages
binSummarization	The method to summarize nucleotides into each bin, either "max" (default), "min" or "mean".
...	Passed to 'ScanBamParam'

Details

* For single-end ChIPseq data, extend reads to the expected fragment size using the 'extend' argument. * The implementation involves reading the reads before processing, which can be quite memory-hungry. To avoid this the files are read by chunks (composed of chromosomes of balanced sizes), controlled by the 'splitByChr' argument. This reduces memory usage but also creates overhead which reduces the speed. In contexts where the file is small or memory isn't a problem, using 'splitByChr=FALSE' will achieve the best speed. Otherwise, increasing 'splitByChr' will decrease the memory footprint. * Consider restricting the read quality using 'includeDuplicates=FALSE' and 'minMapq=20' for example.

Value

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

Author(s)

Pierre-Luc Germain

Examples

# get an example bam file
bam <- system.file("extdata", "ex1.bam", package="Rsamtools")
# create bigwig
bam2bw(bam, "output.bw")

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