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.
read_bed(file_name, tibble = FALSE, ...)
| file_name | Path to the bed file to be read in |
|---|---|
| tibble | logical If TRUE, the genomic intervals are returned as
a tidy |
| ... | Other arguments passed to |
Either a data.frame or a tbl_df with at least three
columns named 'chrom', 'start' and 'end'
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.
bed_path <- system.file("extdata", "Q_centro.bed", package="pafr") centro <- read_bed(bed_path) centro#> chrom start end #> 1 Q_chr1 1305119 1325119 #> 2 Q_chr2 3311000 3331000 #> 3 Q_chr5 1780000 1800000 #> 4 Q_chr6 1005337 1025337 #> 5 Q_chr4 951000 971000 #> 6 Q_chr7 449000 469000 #> 7 Q_chr3 625000 645000# Can pass arguments to read.table miss_two <- read_bed(bed_path, skip=2) miss_two#> chrom start end #> 1 Q_chr5 1780000 1800000 #> 2 Q_chr6 1005337 1025337 #> 3 Q_chr4 951000 971000 #> 4 Q_chr7 449000 469000 #> 5 Q_chr3 625000 645000