getBetas {sesame} | R Documentation

## Get beta Values

### Description

sum.typeI is used for rescuing beta values on Color-Channel-Switching CCS probes. The function takes a `SigSet` and returns beta value except that Type-I in-band signal and out-of-band signal are combined. This prevents color-channel switching due to SNPs.

### Usage

    getBetas(
      sset,
      quality.mask = TRUE,
      nondetection.mask = TRUE,
      correct.switch = TRUE,
      mask.use.tcga = FALSE,
      pval.threshold = 0.05,
      pval.method = NULL,
      sum.TypeI = FALSE
    )

### Arguments

`sset` | `SigSet`
`quality.mask` | whether to mask low quality probes
`nondetection.mask` | whether to mask nondetection
`correct.switch` | whether to correct switch
`mask.use.tcga` | whether to use TCGA masking, only applies to HM450
`pval.threshold` | p-value threshold for nondetection mask
`pval.method` | method for detection threshold, like pOOBAH, PnegEcdf
`sum.TypeI` | whether to sum type I channels

### Value

a numeric vector, beta values

### Examples

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

[Package sesame version 1.5.3 Index]