subgroup_specific_genomic_regions: find subgroup specific regions

Description Usage Arguments Value Examples

View source: R/genomic_region_subgroup_specificity.R

Description

find subgroup specific regions

Usage

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subgroup_specific_genomic_regions(gr, factors,
    present = 0.7, absent = 0.3, type = NULL)

Arguments

gr

a GRanges object coming from common_regions

factors

classes which correspond to samples in gr

present

how to define a common region is specifically present in one subgroup? The subgroup specificity is calculated based on the precent matrix stored in gr. For each subgroup which is defined in factors, if the value is a single numeric value, it means the mean value should be larger than this. It can also be a function for which the input is the vector of percent in corresponding subgroup and the output should be a single logical value.

absent

how to define a common region is specifically absent in one subgroup. Format is same as present

type

It uses a string containing 1 and 0 to represent types of specificity. E.g. '1100' means present in subgroup 1 and 2 while absent in subgroup 3 and 4. By default, it will output all combination of subgroup specificities.

Value

In fact, this function split the original gr into a list in which each element contains regions corresponding to different subgroup specificity.

The returned value can be sent to plot_subgroup_specificity_heatmap to visualize the specificity.

Examples

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# There is no example
NULL

jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.