make_transition_matrix_from_chromHMM: Generate transition matrix from chromHMM results

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Generate transition matrix from chromHMM results

Usage

make_transition_matrix_from_chromHMM(gr_list_1, gr_list_2, window = NULL,
    min_1 = floor(length(gr_list_1)/2), min_2 = floor(length(gr_list_2)/2))

Arguments

gr_list_1	a list of GRanges objects which contain chromatin states in group 1. The first column in meta columns should be the states. Be careful when importing bed files to GRanges objects (start positions in bed files are 0-based while 1-based in GRanges objects.
gr_list_2	a list of GRanges objects which contains chromatin states in group 2.
window	window size which was used to do chromHMM states prediction. If it is not specified, the greatest common divisor of the width of all regions is used.
min_1	If there are multiple samples in group 1, the state assigned to reach region should have recurrency larger or equal to this value.
min_2	same as min_1, but for samples in group 2.

Details

The whole genome is segmentated by size of window and states with highest occurence among samples are assigned to segments.

To make the function run successfully, number of segments in all samples should be all the same and there should not be gaps between regions.

Value

A transition matrix in which values represent total width of regions that transite from one state to the other. Rows correspond to group 1 and columns correspond to group 2.

Author(s)

Zuguang Gu <[e-mail]>

See Also

The matrix can be sent to chromatin_states_transition_chord_diagram to visualize.

Examples

set.seed(123)
gr_list_1 = lapply(1:5, function(i) {
	pos = sort(c(0, sample(1:9999, 99), 10000))*200
	GRanges(seqnames = "chr1", ranges = IRanges(pos[-101] + 1, pos[-1]), 
	    states = paste0("state_", sample(1:9, 100, replace = TRUE)))
})
gr_list_2 = lapply(1:5, function(i) {
	pos = sort(c(0, sample(1:9999, 99), 10000))*200
	GRanges(seqnames = "chr1", ranges = IRanges(pos[-101] + 1, pos[-1]), 
	    states = paste0("state_", sample(1:9, 100, replace = TRUE)))
})
mat = make_transition_matrix_from_chromHMM(gr_list_1, gr_list_2)

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.