countsToVariables {midasHLA} | R Documentation

## Convert counts table to variables

### Description

`countsToVariables` converts counts table to additional variables.

### Usage

    countsToVariables(counts, dictionary, na.value = NA, nacols.rm = TRUE)

### Arguments

`counts` | Data frame with counts, such as returned by `hlaCallsToCounts` function. First column should contain samples IDs, following columns should contain counts (natural numbers including zero).
`dictionary` | Path to file containing variables dictionary or data frame. See details for further explanations.
`na.value` | Vector of length one speciyfing value for variables with no matching entry in `dictionary`. Default is to use `0`.
`nacols.rm` | Logical indicating if result columns that contain only `NA` should be removed.

### Details

`dictionary` file should be a tsv format with header and two columns. First column should be named `"Name"` and hold variable name, second should be named `"Expression"` and hold expression used to identify variable (eg. `"KIR2DL3 & ! KIR2DL2"` will match all samples with `KIR2DL3` and without `KIR2DL2`). Optionally a data frame formatted in the same manner can be passed instead.

Dictionaries shipped with the package:

`kir_haplotypes`

  KIR genes to KIR haplotypes dictionary.

### Value

Data frame with variable number of columns. First column named `"ID"` corresponds to `"ID"` column in `counts`, further columns hold indicators for converted variables. `1` and `0` code presence and absence of a variable respectively.

### Examples

    countsToVariables(MiDAS_tut_KIR, "kir_haplotypes")

[Package midasHLA version 1.2.0 Index]