Iset_region_to_LFM: Convert an InteractionSet region into a ligation frequency...

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

Description

Pick a genomic region from an InteractionSet object and convert it into a sparse triangular matrix.

Usage

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

Arguments

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

Examples

# matrix <- Iset_region_to_matrix(Iset, chr = 11, from = 30000000, to = 30100000)

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