getAFTypeIbySumAlleles {sesame} | R Documentation

## Get allele frequency treating type I by summing alleles

### Description

Takes a `SigSet` as input and returns a numeric vector containing extra allele frequencies based on Color-Channel-Switching (CCS) probes. If no CCS probes exist in the `SigSet`, then an numeric(0) is returned.

### Usage

    getAFTypeIbySumAlleles(sset, known.ccs.only = TRUE)

### Arguments

`sset` | `SigSet`
`known.ccs.only` | consider only known CCS probes

### Value

beta values

### Examples

    sset <- sesameDataGet('EPIC.1.LNCaP')$sset
    betas <- getAFTypeIbySumAlleles(sset)

[Package sesame version 1.5.3 Index]