testNeutral {MesKit} | R Documentation

## testNeutral

### Description

Evaluate whether a tumor follows neutral evolution or under strong selection during the growth based on variant frequency distribution (VAF) of subclonal mutations. The subclonal mutant allele frequencies of a follow a simple power-law distribution predicted by neutral growth.

### Usage

    testNeutral(
      maf,
      patient.id = NULL,
      withinTumor = FALSE,
      min.total.depth = 2,
      min.vaf = 0.1,
      max.vaf = 0.3,
      R2.threshold = 0.98,
      min.mut.count = 20,
      plot = TRUE,
      use.tumorSampleLabel = FALSE,
      ...
    )

### Arguments

`maf` | Maf or MafList object generated by `readMaf` function.
`patient.id` | Select the specific patients. Default NULL, all patients are included.
`withinTumor` | Test neutral within tumros in each patients. Default FALSE.
`min.total.depth` | The minimun total depth of coverage. Defalut 2
`min.vaf` | The minimum value of adjusted VAF value. Default 0.1
`max.vaf` | The maximum value of adjusted VAF value. Default 0.3
`R2.threshold` | The threshod of R2 to decide whether a tumor follows neutral evolution. Default 0.98
`min.mut.count` | The minimun number of subclonal mutations used to fit model. Default 20
`plot` | Logical, whether to print model fitting plot of each sample. Default TRUE.
`use.tumorSampleLabel` | Let Tumor_Sample_Barcode replace Tumor_Sample_Label if Tumor Label is provided in clinical data. Default FALSE.
`...` | Other options passed to `subMaf`

### Value

the neutrality metrics and model fitting plots

### References

Williams, M., Werner, B. et al. Identification of neutral tumor evolution across cancer types. Nat Genet 48, 238-244 (2016)

### Examples

    maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
    clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
    ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
    maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
    testNeutral(maf)

[Package MesKit version 1.4.0 Index]