getSexFromVcf {PureCN} | R Documentation

## Get sample sex from a VCF file

### Description

This function detects non-random distribution of homozygous variants on chromosome X compared to all other chromosomes. A non-significant Fisher's exact p-value indicates more than one chromosome X copy. This function is called in runAbsoluteCN as sanity check when a VCF is provided. It is also useful for determining sex when no sex marker genes on chrY (e.g. AMELY) are available.

### Usage

    getSexFromVcf(
      vcf,
      tumor.id.in.vcf = NULL,
      min.or = 4,
      min.or.na = 2.5,
      max.pv = 0.001,
      homozygous.cutoff = 0.95,
      af.cutoff = 0.2,
      min.coverage = 15,
      use.somatic.status = TRUE
    )

### Arguments

`vcf` | CollapsedVCF object, read in with the `readVcf` function from the VariantAnnotation package.
`tumor.id.in.vcf` | The tumor id in the CollapsedVCF (optional).
`min.or` | Minimum odds-ratio to call sample as male. If p-value is not significant due to a small number of SNPs on chromosome X, sample will be called as NA even when odds-ratio exceeds this cutoff.
`min.or.na` | Minimum odds-ratio to not call a sample. Odds-ratios in the range `min.or.na` to `min.or` define a grey area in which samples are not called. Contamination can be a source of ambiguous calls.
`max.pv` | Maximum Fisher's exact p-value to call sample as male.
`homozygous.cutoff` | Minimum allelic fraction to call position homozygous.
`af.cutoff` | Remove all SNVs with allelic fraction lower than the specified value.
`min.coverage` | Minimum coverage in tumor. Variants with lower coverage are ignored.
`use.somatic.status` | If somatic status and germline data is available, then exclude somatic variants.

### Value

Returns a `character(1)` with `M` for male, `F` for female, or `NA` if unknown.

### Author(s)

Markus Riester

### See Also

`getSexFromCoverage`

### Examples

    vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
    vcf <- readVcf(vcf.file, "hg19")
    # This example vcf is filtered and contains no homozygous calls,
    # which are necessary for determining sex from chromosome X.
    getSexFromVcf(vcf)

[Package PureCN version 2.0.2 Index]