HodgesTools (version 1.0.0)

read_bed: 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)

Value

tibble

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

Author

Tyler Hansen & Tim Scott

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).

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"))