signal2Matrix: signal2Matrix: reads the signals in/around a set of genomic...

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

signal2Matrix: reads the signals in/around a set of genomic regions.

Description

Reads the signals from bam/bigwig files within and/or around (the centers of) a set of regions, and outputs an EnrichmentSE object.

Usage

signal2Matrix(
  filepaths,
  regions,
  extend = 2000,
  w = NULL,
  scaling = TRUE,
  scaledBins = round(max(extend)/w),
  type = c("center", "scaled"),
  binMethod = c("mean", "max", "min"),
  BPPARAM = 1L,
  ret = c("EnrichmentSE", "list"),
  verbose = TRUE,
  ...
)

Arguments

filepaths	A named vector of filepaths (e.g. to bigwig files; bam files are also supported, but with limited functionalities). Can also be a named list including a combination of paths to such files and 'GRanges' object. For 'GRanges' objects, the 'score' column will be used (absolute coverage mode).
regions	A 'GRanges' of the regions/positions around which to plot, or the path to a bed file of such regions. If 'type="scaled"', 'regions' can also be a 'GRangesList', in which case the coverage of the subregions will be stiched together (e.g. for plotting exonic signal over transcripts).
extend	Number of basepair to extend on either side of the regions. Must be a multiple of 'w'. Can also be an integer of length 2, indicating the extension upstream and downstream.
w	Bin width in number of nucleotides. Defaults to a width producing 200 bins over the whole extended range.
scaledBins	The number of bins for the scale region (ignored if 'type="center"')
type	Either 'center' (plots fixed-size region around the centers of ‘regions') or ’scaled' (scales the signal in 'regions' and plot surroundings)
binMethod	Whether to compute the 'max' (default), 'mean' or 'min' per bin.
BPPARAM	A BiocParallelParam object, or the number of threads to use to read and prepare the data. Note that the rate-limiting process is reading from disk, so unless you have an unusually fast disk, using multi-threading is actually likely to slow down rather than speed up the process.
ret	The type of output to return, either an "EnrichmentSE" object (default), or a simple list of signal matrices ("list").
verbose	Logical; whether to print processing information
...	Passed to normalizeToMatrix or as.normalizedMatrix, or to bam2bw when reading bam files. For example, this can be used to pass arguments to 'normalizeToMatrix' such as 'smooth=TRUE'.

Value

A list of 'normalizeToMatrix' objects

Examples

# we fetch the path to the example bigwig file:
(bw <- system.file("extdata/example_atac.bw", package="epiwraps"))
# we load example regions:
regions <- rtracklayer::import(system.file("extdata/example_peaks.bed", 
                                           package="epiwraps"))
length(regions)
# we obtain the matrix of the signal around the regions:
m <- signal2Matrix(bw, regions)
# we can plot it with:
plotEnrichedHeatmaps(m)
# we could also take a broader range around the center of the regions, and 
# use bigger bins:
m <- signal2Matrix(bw, regions, extend=2000, w=20)
plotEnrichedHeatmaps(m)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.