AllelicImbalance (version 1.10.2)

initialize-DetectedAI: 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

Examples

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