readHlaCalls {midasHLA} | R Documentation

## Read HLA allele calls

### Description

`readHlaCalls` read HLA allele calls from file

### Usage

    readHlaCalls(file, resolution = 4, na.strings = c("Not typed", "-", "NA"))

### Arguments

`file` | Path to input file.
`resolution` | Number specifying desired resolution.
`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 with a header. First column should contain sample IDs, further columns hold HLA allele numbers. See `system.file("extdata", "MiDAS_tut_HLA.txt", package = "midasHLA")` file for an example.

`resolution` parameter can be used to reduce HLA allele numbers. If reduction is not needed `resolution` can be set to 8. `resolution` parameter can take the following values: 2, 4, 6, 8. For more details about HLA allele numbers resolution see http://hla.alleles.org/nomenclature/naming.html.

### Value

HLA calls data frame. First column hold sample IDs, further columns hold HLA allele numbers.

### Examples

    file <- system.file("extdata", "MiDAS_tut_HLA.txt", package = "midasHLA")
    hla_calls <- readHlaCalls(file)

[Package midasHLA version 1.2.0 Index]