get_genomic_annotations: Annotate genomic regions

In itsvenu/ALPS: AnaLysis routines for ePigenomicS data

Description

annotate genomic regions by simultaneosuly merging overlaping regions and preparing consensus set of genomic regions from multiple files

Usage

get_genomic_annotations(data_table, ref_gen = "hg38",
  tss_region = c(-1000, 1000), merge_level = "all")

Arguments

data_table	a data.frame of sample table, as is for multiBigwig_summary input table, default NULL
ref_gen	reference genome, either hg38 or hg19, default hg38
tss_region	bp ± TSS to define promoter regions
merge_level	either all, group_level or none. all prepares a consensus set of peaks from all files present in data_table. group_level prepares consensus set of peaks from all samples present each group separately. none does not prepare any consensus peak set, annotates each peak file separately. Default all

Value

a data.frame of annotations and percentages

Examples

chr21_data_table <- system.file('extdata/bw', 'ALPS_example_datatable.txt', package = 'ALPS', mustWork = TRUE)

## attach path to bw_path and bed_path
d_path <- dirname(chr21_data_table)

chr21_data_table <- read.delim(chr21_data_table, header = TRUE)
chr21_data_table$bw_path <- paste0(d_path, '/', chr21_data_table$bw_path)
chr21_data_table$bed_path <- paste0(d_path, '/', chr21_data_table$bed_path)

get_genomic_annotations(data_table = chr21_data_table,
merge_level = 'group_level')

itsvenu/ALPS documentation built on Nov. 4, 2019, 2:13 p.m.