basic_genomic_regions_stat: Basic statistics on genomic regions

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

Description

Basic statistics on genomic regions

Usage

basic_genomic_regions_stat(gr_list, annotation = NULL, annotation_color = NULL,
    main = NULL, species = "hg19", type = c("proportion", "number", "median_width"),
    by_chr = FALSE)

Arguments

gr_list	a list of GRanges.
annotation	a vector which contains class of samples. If it has names which correspond to gr_list, the order of this vector is automatically adjusted.
annotation_color	colors corresponding to classes of annotations
main	title of the plot
species	species, necessary if type is set to proportion.
type	type of statistics
by_chr	take all chromosomes as a whole or calculate statistics for every chromosome

Details

The function makes barplot to visualize different statistics in all samples.

For type settings:

proportion

proportion of total length of regions compared to the whole genome. It is more unbiased.

number

number of regions. Sometimes only looking at the number of regions gives biased estimation of amount of regions if the width of regions are very viarable.

median_width

median width of regions

Value

A data frame which contains statistics for each chromosome in each sample.

Author(s)

Zuguang Gu <[e-mail]>

Examples

require(circlize)
set.seed(123)
gr_list = lapply(1:10, function(i) {
	df = generateRandomBed(1000)[1:sample(100:1000, 1), ]
	GRanges(df[[1]], ranges = IRanges(df[[2]], df[[3]]))
})
basic_genomic_regions_stat(gr_list)
basic_genomic_regions_stat(gr_list, annotation = rep(letters[1:2], each = 5), 
    annotation_color = c("a" = "red", "b" = "blue"))
basic_genomic_regions_stat(gr_list, annotation = rep(letters[1:2], each = 5), 
    annotation_color = c("a" = "red", "b" = "blue"), type = "number")
basic_genomic_regions_stat(gr_list, annotation = rep(letters[1:2], each = 5), 
    annotation_color = c("a" = "red", "b" = "blue"), type = "median_width")
basic_genomic_regions_stat(gr_list, annotation = rep(letters[1:2], each = 5), 
    annotation_color = c("a" = "red", "b" = "blue"), by_chr = TRUE)

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