initialize-DetectedAI {AllelicImbalance} | R Documentation

## Initialize DetectedAI

### Description

Functions to construct DetectedAI objects

### Usage

    DetectedAIFromArray(x = "ASEset", strand = "*",
      reference.frequency = NULL, threshold.frequency = NULL,
      threshold.count.sample = NULL, threshold.delta.frequency = NULL,
      threshold.pvalue = NULL, threshold.frequency.names = NULL,
      threshold.count.sample.names = NULL,
      threshold.delta.frequency.names = NULL, threshold.pvalue.names = NULL,
      ...)

### Arguments

`x` | `ASEset`
`strand` | set strand to detectAI over "+","-","*"
`reference.frequency` | frequencies of reference alleles based allele counts
`threshold.frequency` | logical array for frequency thresholds
`threshold.count.sample` | logical array for per sample allele count thresholds
`threshold.delta.frequency` | logical array for delta frequency thresholds.
`threshold.pvalue` | logical array for pvalue thresholds (max 1, min 0)
`threshold.frequency.names` | character vector
`threshold.count.sample.names` | character vector
`threshold.delta.frequency.names` | character vector
`threshold.pvalue.names` | character vector
`...` | internal arguments

### Details

produces a class container for reference bias calculations

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    data(ASEset)
    a <- ASEset
    dai <- detectAI(a)

[Package AllelicImbalance version 1.20.0 Index]