importBedScore: importBedScore

In caleblareau/gchromVAR: Compute cell-type specific enrichments with high resolution

Description

Given a set of peaks (GRanges object) and a vector of one or more file paths of .bed files with some score, import these and summarize using a FUN over them. Also can specify which column the score should be read from in the file and the default value per peak if nothing is determined.

Usage

importBedScore(ranges, files, colidx = 5, FUN = sum, default.val = 0)

## S4 method for signature 'GRanges,character'
importBedScore(ranges, files, colidx = 5,
  FUN = sum, default.val = 0)

Arguments

ranges	A GRanges object corresponding to the peaks used to aggregrate a score over
files	A character vector of files that will be imported and digested for analysis
colidx	The column index of the score. This assumes that the first three columns specific genomic coordinates. Default is 5 for the fifth column in the .bed files
FUN	Function to summarize multiple hits in the .bed file over the peak.
default.val	Default value to populate the matrices ahead of time. By default, 0.

Methods (by class)

• ranges = GRanges,files = character:

Author(s)

Caleb Lareau

Examples

files <- list.files(system.file('extdata',package='gchromVAR'), pattern = "*.bed$",
 full.names = TRUE)
data(mini_counts, package = "chromVAR")
w_se <- importBedScore(SummarizedExperiment::rowRanges(mini_counts), files)

caleblareau/gchromVAR documentation built on Jan. 16, 2020, 3:07 p.m.