read_fam: Read Plink *.fam files

In genio: Genetics Input/Output Functions

Read Plink *.fam files

Description

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

Usage

read_fam(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 *.fam extension, the function adds the .fam extension and uses that path if that file exists. Additionally, the .gz extension is added automatically if the file (after *.fam 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: fam, id, pat, mat, sex, pheno.

See Also

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

Plink FAM format reference: https://www.cog-genomics.org/plink/1.9/formats#fam

Examples

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

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

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

# can specify without extension
file <- sub('\\.fam$', '', file) # remove extension from this path on purpose
file # verify .fam is missing
fam <- read_fam(file) # load it anyway!
fam

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