read_bim: Read Plink *.bim files

In genio: Genetics Input/Output Functions

Read Plink *.bim files

Description

This function reads a standard Plink *.bim file into a tibble with named columns. It uses readr::read_table() to do it efficiently.

Usage

read_bim(file, verbose = TRUE)

Arguments

file

Input file (whatever is accepted by readr::read_table()). If file as given does not exist and is missing the expected *.bim extension, the function adds the .bim extension and uses that path if that file exists. Additionally, the .gz extension is added automatically if the file (after *.bim extension is added as needed) is still not found and did not already contain the .gz extension and adding it points to an existing file.

verbose

If TRUE (default) function reports the path of the file being loaded (after autocompleting the extensions).

Value

A tibble with columns: chr, id, posg, pos, alt, ref.

See Also

read_plink() for reading a set of BED/BIM/FAM files.

Plink BIM format references: https://www.cog-genomics.org/plink/1.9/formats#bim https://www.cog-genomics.org/plink/2.0/formats#bim

Examples

# to read "data.bim", run like this:
# bim <- read_bim("data")
# this also works
# bim <- read_bim("data.bim")

# The following example is more awkward
# because package sample data has to be specified in this weird way:

# read an existing Plink *.bim file
file <- system.file("extdata", 'sample.bim', package = "genio", mustWork = TRUE)
bim <- read_bim(file)
bim

# can specify without extension
file <- sub('\\.bim$', '', file) # remove extension from this path on purpose
file # verify .bim is missing
bim <- read_bim(file) # loads too!
bim

genio documentation built on Jan. 7, 2023, 1:12 a.m.