read_snp: Read Eigenstrat *.snp files

In genio: Genetics Input/Output Functions

Read Eigenstrat *.snp files

Description

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

Usage

read_snp(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 *.snp extension, the function adds the .snp extension and uses that path if that file exists. Additionally, the .gz extension is added automatically if the file (after *.snp 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, chr, posg, pos, ref, alt

See Also

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

Examples

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

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

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

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

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