getProfileData-methods: Get Profile Data surrounding specified ranges

In steveped/chipExtra: Additional functions for working with ChIP-Seq data

Get Profile Data surrounding specified ranges

Description

Get coverage Profile Data surrounding specified ranges

Usage

getProfileData(x, gr, ...)

## S4 method for signature 'BigWigFile,GenomicRanges'
getProfileData(
  x,
  gr,
  upstream = 2500,
  downstream = upstream,
  bins = 100,
  mean_mode = "w0",
  log = TRUE,
  offset = 1,
  n_max = Inf,
  ...
)

## S4 method for signature 'BigWigFileList,GenomicRanges'
getProfileData(
  x,
  gr,
  upstream = 2500,
  downstream = upstream,
  bins = 100,
  mean_mode = "w0",
  log = TRUE,
  offset = 1,
  BPPARAM = SerialParam(),
  ...
)

## S4 method for signature 'character,GenomicRanges'
getProfileData(
  x,
  gr,
  upstream = 2500,
  downstream = upstream,
  bins = 100,
  mean_mode = "w0",
  log = TRUE,
  offset = 1,
  ...
)

Arguments

x	A BigWigFile or BigWiFileList
gr	A GRanges object
...	Passed to normalizeToMatrix
upstream	The distance to extend upstream from the centre of each range within gr
downstream	The distance to extend downstream from the centre of each range within gr
bins	The total number of bins to break the extended ranges into
mean_mode	The method used for calculating the score for each bin. See normalizeToMatrix for details
log	logical(1) Should the returned values be log2-transformed
offset	Value added to data if log-transforming. Ignored otherwise
n_max	Upper limit on the number of ranges to return profile data for. By default, no limit will be applied .
BPPARAM	Passed internally to bplapply

Details

This will take all provided ranges and set as identical width ranges, extending by the specified amount both up and downstream of the centre of the provided ranges. By default, the ranges extensions are symmetrical and only the upstream range needs to be specified, however this parameterisation allows for non-symmetrical ranges to be generated.

These uniform width ranges will then be used to extract the value contained in the score field from one or more BigWigFiles. Uniform width ranges are then broken into bins of equal width and the average score found within each bin.

The binned profiles are returned as a DataFrameList called profile_data as a column within the resized GRanges object. Column names in each DataFrame are score, position and bp.

If passing a BigWigFileList, profiles will be obtained in series by default. To run in parallel pass a MulticoreParam object to the BPPARAM argument.

Value

GRanges or GrangesList with column profile_data, as described above

Examples

bw <- system.file("tests", "test.bw", package = "rtracklayer")
gr <- GRanges("chr2:1000")
pd <- getProfileData(bw, gr, upstream = 500, bins = 10)
pd
pd$profile_data

steveped/chipExtra documentation built on Aug. 1, 2024, 12:33 a.m.