read_bed {HodgesTools}

Read bed file

Description

Reads in a tab-delimited BED formatted file into R.

Usage

read_bed(file, extra_col_names = c(), length = FALSE, verbose = TRUE)

Arguments

file

bed file

extra_col_names

list of strings specifying extra column names

length

boolean of whether to add length column

verbose

boolean set to see function behavior

Details

First three columns of file must be the genomic coordinates of the regions (i.e. chr start end).

read_bed will auto-detect BED3 and BED6 formats. It will also detect BED3+ and BED6+ formats assigning generic or user-defined col_names to the additional column(s).

Value

tibble

Author(s)

Tyler Hansen & Tim Scott

Examples

#load external data.
BED3 <- system.file(package = "HodgesTools", "extdata", "test_BED3.bed")
BED6 <- system.file(package = "HodgesTools", "extdata", "test_BED6.bed")
BED4 <- system.file(package = "HodgesTools", "extdata", "test_BED4.bed")
BED8 <- system.file(package = "HodgesTools", "extdata", "test_BED8.bed")

# Read 3-column BED file.
read_bed(BED3)

# Read 6-column BED file.
read_bed(BED6)

# Read 3-column BED file and add length column.
read_bed(BED3, length = TRUE)

# Read 3 column format BED file with additional fourth column. Add generic column names.
read_bed(BED4)

# Read 3 column format BED file with additional fourth column. Specify additional column names.
read_bed(BED4, extra_col_names = c("fourthColumn"))

# Read 6 column format BED file with additional columns. Specify additional column names.
read_bed(BED8, extra_col_names = c("seventhColumn", "eigthColumn"))