readKirCalls: Read KIR calls

In Genentech/MiDAS: R package for immunogenomics data handling and association analysis

Read KIR calls

Description

readKirCalls read KIR calls from file.

Usage

readKirCalls(file, na.strings = c("", "NA", "uninterpretable"))

Arguments

file	Path to input file.
na.strings	a character vector of strings which are to be interpreted as NA values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. Note that the test happens after white space is stripped from the input, so na.strings values may need their own white space stripped in advance.

Details

Input file has to be a tsv formatted table. First column should be named "ID" and contain samples IDs, further columns should hold KIR genes presence / absence indicators. See system.file("extdata", "MiDAS_tut_KIR", package = "midasHLA") for an example.

Value

Data frame containing KIR gene's counts. First column hold samples IDs, further columns hold KIR genes presence / absence indicators.

Examples

file <- system.file("extdata", "MiDAS_tut_KIR.txt", package = "midasHLA")
readKirCalls(file)

Genentech/MiDAS documentation built on Feb. 5, 2024, 11:52 a.m.