initialize-DetectedAI: Initialize DetectedAI

In AllelicImbalance: Investigates Allele Specific Expression

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)

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.