mapGrlCols: Collapse a GRangesList adding multiple columns from each...

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

Collapse a GRangesList adding multiple columns from each element

Description

Make consensus peaks and add individual columns from each original GRangesList element

Usage

mapGrlCols(
  x,
  var = NULL,
  collapse = NULL,
  collapse_sep = "; ",
  name_sep = "_",
  include = FALSE,
  ...
)

Arguments

x	GRangesList
var	Column(s) to map onto the set of consensus peaks
collapse	Columns specified here will be simplified into a single column. Should only be character or factor columns
collapse_sep	String to separate values when collapsing columns
name_sep	String to separate values when adding column names
include	logical(1) Include the original ranges as character columns
...	Passed to makeConsensus

Details

Starting with a GRangesList, make a single GRanges object with select columns from each element added to the new object

Value

GRanges object with a set of consensus ranges across all list elements and values from each element mapped to these consensus ranges.

If requested (include = TRUE) the original ranges are returned as character columns, as there will be multiple NA values in each.

Examples

a <- GRanges(paste0("chr1:", seq(1, 61, by = 20)))
width(a) <- 5
a$logFC <- rnorm(length(a))
a_g <- as.list(paste("Gene", seq_along(a)))
a_g[[1]] <- c("Gene 0", a_g[[1]])
a$genes <- as(a_g, "CompressedList")

b <- GRanges("chr1:61-70")
b$logFC <- rnorm(1)
b$genes <- as(list("Gene 5"), "CompressedList")

grl <- GRangesList(A = a, B = b)
mapGrlCols(grl, var = "logFC")

## This forms a union of overlapping rangesby default
## Pass methods to makeConsensus() to change to regions with coverage == 2
mapGrlCols(grl, var = "logFC", method = "coverage", p = 1)

## Columns can be collapsed to merge into a single column
mapGrlCols(grl, var = "logFC", collapse = "genes")

## Original ranges can also be included
mapGrlCols(grl, collapse = "genes", include = TRUE)

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