enrichment_by_significance: Enrichment of rare variants stratified by outlier...
In jeinson/ExOutBench: [Ex]pression [Out]lier [Bench]marking tool

Description Usage Arguments Value

View source: R/enrichment_functions.R

Enrichment of rare variants stratified by outlier significance threshold

enrichment_by_significance(outlier.calls, rare.variants,
  outlier.thresholds = c(0.05, 0.01, 0.001, 1e-04, 1e-05, 1e-07),
  limit.to.genes.w.outliers = T, base.significance.cutoff = 0.05,
  draw.plot = T, verbose = T)

`outlier.calls`	A data frame with columns `GeneID`, `SampleName`, and `outlier.score`. The outlier.score is the result of any expression based test which designates a gene as an outlier at some threshold.
`rare.variants`	A data frame that lists all rare variants found near individual-gene pairs. Must columsn titled `SampleName`, `GeneID`, `chr`, `start`, and `end`
`outlier.thresholds`	Defaults to 'c(0.05, 1e-2, 1e-3, 1e-4, 1e-5, 1e-7)'. This script will calculate enrichment at every threshold.
`limit.to.genes.w.outliers`	Default to 'TRUE'. Should I remove genes that are never outliers in any individual?
`base.significance.cutoff`	Default to '0.05'. Only needed if 'limit.to.genes.w.outliers' is true. Use this threshold for deciding whether to exclude genes that are never outliers.
`verbose`	Defaults to 'TRUE' Should I print annoying but helpful messages?

A data frame with enrichment scores at each significance level.

This function takes a data frame of outlier calls and a data frame of rare variant genotype data and produces a data frame with enrichment values representing the relative risk of having a rare variant given outlier status at different significance levels.

jeinson/ExOutBench documentation built on Nov. 4, 2019, 2:38 p.m.