hilbert_curve_chipseq_difference: Visualize ChIP-Seq signal difference by Hilbert curve

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Visualize ChIP-Seq signal difference by Hilbert curve

Usage

hilbert_curve_chipseq_difference(mark, subgroup, comparison, chromosome = paste0("chr", 1:22),
    species = "hg19", type = c("global_mean", "subgroup_mean", "abs_difference", "rel_difference"))

Arguments

mark	name of the histone mark, should also be supported in chipseq_hooks
subgroup	subgroup information which corresponds to sample IDs stored in chipseq_hooks$sample_id. The value should be a named vector that names are sample IDs.
comparison	if there are more than one subgroups, the comparison of two subgroups which shows the difference The value is a vector of length of two and the difference is calculated as subgroup[1] - subgroup[2]
chromosome	a vector fo chromosome names
species	species
type	four types of visualization supported, see "details" section

Details

Genome is segmented by 1kb window and mean signal for each 1kb window is calculated, later visualized by Hilbert curve.

There are four types of visualization methods:

global_mean

the mean signal averaged from all samples

subgroup_mean

the mean signal averaged in every subgroup

abs_difference

the absolute difference of signal in two subgroups

rel_difference

the relative difference in two subgroups. The value is calculated as absolute difference divided by mean singal.

Value

a GRanges object which contains mean signal for the 1kb segments and other statistics.

The returned value can be sent to general_chipseq_association_to_methylation and general_chipseq_association.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.