importPeaks: Import peaks

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

Import peaks

Description

Import peaks in narrowPeak, broadPeak or bed format

Usage

importPeaks(
  x,
  type = c("narrow", "broad", "bed"),
  blacklist,
  seqinfo,
  pruning.mode = c("coarse", "error"),
  sort = TRUE,
  setNames = TRUE,
  glueNames = "{basename(x)}",
  centre = FALSE,
  nameRanges = TRUE,
  ...
)

Arguments

x	One or more files to be imported. All files must be of the same type, i.e. narrow or broad
type	The type of peaks to be imported
blacklist	A set of ranges to be excluded
seqinfo	A seqinfo object to be applied to the GRanges objects
pruning.mode	How to handle conflicts if supplying a seqinfo object. Defaults to pruning.mode = "coarse". Only "coarse" and "error" are implemented. See seqinfo.
sort	logical. Should the ranges be sorted during import
setNames	logical Set basename(x) as the name for each element of the GRangesList
glueNames	glue syntax for naming list elements
centre	Add the estimated peak centre. Ignored unless type = "narrow"
nameRanges	Place any values in the name column as range names within each file.
...	passed to sort

Details

Peaks are imported from narrowPeak, broadPeak or bed format as GenomicRanges objects.

If importing bed files, only the default 3-6 columns will imported.

Value

A GRangesList

Examples

fl <- system.file(
    c("extdata/ER_1.narrowPeak", "extdata/ER_2.narrowPeak"),
    package = "extraChIPs"
)
peaks <- importPeaks(fl)
peaks

steveped/chipExtra documentation built on May 2, 2024, 12:11 p.m.