read_ind: Read Eigenstrat *.ind files

In genio: Genetics Input/Output Functions

Read Eigenstrat *.ind files

Description

This function reads a standard Eigenstrat *.ind file into a tibble. It uses readr::read_table() to do it efficiently.

Usage

read_ind(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 *.ind extension, the function adds the .ind extension and uses that path if that file exists. Additionally, the .gz extension is added automatically if the file (after *.ind 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: id, sex, label.

See Also

Eigenstrat IND format reference: https://github.com/DReichLab/EIG/tree/master/CONVERTF

Examples

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

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

# read an existing Eigenstrat *.ind file
file <- system.file("extdata", 'sample.ind', package = "genio", mustWork = TRUE)
ind <- read_ind(file)
ind

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

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