get_genomic_annotations {ALPS} | R Documentation |
annotate genomic regions by simultaneosuly merging overlaping regions and preparing consensus set of genomic regions from multiple files
get_genomic_annotations(data_table, ref_gen = "hg38", tss_region = c(-1000, 1000), merge_level = "all")
data_table |
a data.frame of sample table, as is for
|
ref_gen |
reference genome, either |
tss_region |
bp ± TSS to define promoter regions |
merge_level |
either |
a data.frame of annotations and percentages
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')