vafCompare {maftools} | R Documentation

## compare VAF across two cohorts

### Description

Draw boxplot distibution of VAFs across two cohorts

### Usage

    vafCompare(
      m1,
      m2,
      genes = NULL,
      top = 5,
      vafCol1 = NULL,
      vafCol2 = NULL,
      m1Name = "M1",
      m2Name = "M2",
      cols = c("#2196F3", "#4CAF50"),
      sigvals = TRUE,
      nrows = NULL,
      ncols = NULL
    )

### Arguments

`m1` | first `MAF` object. Required.
`m2` | second `MAF` object. Required.
`genes` | specify genes for which plot has to be generated. Default NULL.
`top` | if `genes` is NULL plots top n number of genes. Defaults to 5.
`vafCol1` | manually specify column name for vafs in `m1`. Default looks for column 't_vaf'
`vafCol2` | manually specify column name for vafs in `m2`. Default looks for column 't_vaf'
`m1Name` | optional name for first cohort
`m2Name` | optional name for second cohort
`cols` | vector of colors corresponding to `m1` and `m2` respectivelly.
`sigvals` | Estimate and add significance stars. Default TRUE.
`nrows` | Number of rows in the layout. Default NULL - estimated automatically
`ncols` | Number of genes drawn per row. Default 4

[Package maftools version 2.4.12 Index]