easy_Iset_to_LFM: Convert an InteractionSet into a sparse, upper triangle...

In AnnikaGable/chromium: Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET

Description

Wrapper for Iset_to_LFM (no subsetting) and Iset_region_to_LFM (subsetting by chromosome and, if required, by region).

Usage

easy_Iset_to_LFM(Iset, chr = NULL, from = NULL, to = NULL)

Arguments

Iset	An interactionSet object, with the bin size stored as metadata under the name 'binSize'.
chr	Optional. The chromosome name to be plotted with or without 'chr', depending on your interactionSet object.
from	Optional. Start of the region you want to select. If NULL, the start of the chromosome will be 'from'.
to	Optional. End of the region you want to select. If NULL, the end of the chromosome will be 'to'.

Value

A sparse, upper triangle ligation frequency matrix.

Examples

# LFM <- easy_Iset_to_LFM(Iset)
# chr2_1_300000 <- easy_Iset_to_LFM(Iset, chr = 2, from = 1, to = 300000)

AnnikaGable/chromium documentation built on May 5, 2019, 6:04 a.m.