read_bed {pafr}

Read genomic intervals in bed format

Description

The first three columns of the file specified by file_name must contain data in the standard bed format (i.e., a genomic interval represented by 0-based half-open interval with seq-id, start and end position). These columns will be renamed to 'chrom', 'start' and 'end', respectively. Any other columns present in the data will be left unmodified.

Usage

read_bed(file_name, tibble = FALSE, ...)

Arguments

file_name

Path to the bed file to be read in

tibble

logical If TRUE, the genomic intervals are returned as a tidy tbl_df.

...

Other arguments passed to read.table

Details

The file is read into memory with read.table, with the argument sep set to '\t' and stringsAsFactors set to FALSE. All other arguments are left as default, but arguments can be passed from read_bed to read.table.

Value

Either a data.frame or a tbl_df with at least three columns named 'chrom', 'start' and 'end'

Examples

bed_path <- system.file("extdata", "Q_centro.bed", package="pafr")
centro <- read_bed(bed_path)
centro
# Can pass arguments to read.table
miss_two <- read_bed(bed_path, skip=2)
miss_two