count_fragment_overlaps: Count the number of times a list of GenomicRanges objects...

In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description

Count the number of times a list of GenomicRanges objects overlaps another list of GenomicRanges objects.

Usage

count_fragment_overlaps(fragment_list, target_GRanges, binarize = TRUE,
  aggregate = FALSE)

Arguments

fragment_list	The list object containing GenomicRanges objects.
target_GRanges	A second list of GenomicRanges objects.
binarize	Logical indicating whether to retain count values for each region on count overlaps as binary. Default is TRUE.
aggregate	Logical indicating whether to return a matrix of counts or a vector of count sums.

Value

If aggregate == TRUE, a vector with the total count of overlaps between each object in fragment_list and all objects in target_GRanges. If aggregate == FALSE, a matrix with count values for overlaps between each object in fragment_list (as columns) and each object in target_GRanges (as rows).

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.