read_eigenvec: Read Plink eigenvec file
In genio: Genetics Input/Output Functions

read_eigenvec

R Documentation

Read Plink eigenvec file

Description

This function reads a Plink eigenvec file, parsing columns strictly. First two must be 'fam' and 'id', which are strings, and all remaining columns (eigenvectors) must be numeric.

Usage

read_eigenvec(
  file,
  ext = "eigenvec",
  plink2 = FALSE,
  comment = if (plink2) "" else "#",
  verbose = TRUE
)

Arguments

`file`	The input file path, potentially excluding extension.
`ext`	File extension (default "eigenvec") can be changed if desired. Set to `NA` to force `file` to exist as-is.
`plink2`	If `TRUE`, the header is parsed and preserved in the returned data. The first two columns must be FID and IID, which are mandatory.
`comment`	A string used to identify comments. Any text after the comment characters will be silently ignored. Passed to `readr::read_table()`. '#' (default when `plink2 = FALSE`) works for Plink 2 eigenvec files, which have a header lines that starts with this character (the header is therefore ignored). However, `plink2 = TRUE` forces the header to be parsed instead.
`verbose`	If `TRUE` (default) function reports the path of the file being written (after autocompleting the extension).

Value

A list with two elements:

eigenvec: A numeric R matrix containing the parsed eigenvectors. If plink2 = TRUE, the original column names will be preserved in this matrix.
fam: A tibble with two columns, fam and id, which are the first two columns of the parsed file. These column names are always the same even if plink2 = TRUE (i.e. they won't be FID or IID).

Examples

# to read "data.eigenvec", run like this:
# data <- read_eigenvec("data")
# this also works
# data <- read_eigenvec("data.eigenvec")
#
# either way you get a list with these two items:
# numeric eigenvector matrix
# data$eigenvec
# fam/id tibble
# data$fam

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

# read an existing *.eigenvec file created by GCTA
file <- system.file("extdata", 'sample-gcta.eigenvec', package = "genio", mustWork = TRUE)
data <- read_eigenvec(file)
# numeric eigenvector matrix
data$eigenvec
# fam/id tibble
data$fam

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

# read an existing *.eigenvec file created by Plink 2
file <- system.file("extdata", 'sample-plink2.eigenvec', package = "genio", mustWork = TRUE)
# this version ignores header
data <- read_eigenvec(file)
# numeric eigenvector matrix
data$eigenvec
# fam/id tibble
data$fam

# this version uses header
data <- read_eigenvec(file, plink2 = TRUE)
# numeric eigenvector matrix
data$eigenvec
# fam/id tibble
data$fam

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