compare_fragment_lists: Compare two lists of GRanges to get counts or overlap...
In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description Usage Arguments Details Value

If mode = "counts", generates a matrix for the number of overlaps between each set of query and target GRanges. Normalization parameters specify whether to divide by the number of regions in the query, target, or the sum of both (total).

1 2	compare_fragment_lists(query_regions, target_regions, mode = c("counts", "coverage"), norm = c("none", "query", "target", "total"))

`query_regions`	a list of GRanges objects
`target_regions`	a second list of GRanges objects
`mode`	Either "counts" or "coverage".
`norm`	Normalization mode: "none", "query","target", or "total".

If mode = "coverage", generates a matrix with the total number of overlapping bases between each set of query and target GRanges. Normalization parameters specify whether to divide by the total coverage of regions in the query, target, or the sum of both (total).

a matrix with query regions as rows and target regions as columns.

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