ci-utils: CI Utils

In Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

Description

Utility functions to find confidence intervals that (a) overlap a certain value ('ciOutside', 'ciCovers') and (b) different confidence intervals overlap ('ciOverlap').

Usage

  ciOutside(x, delta = 0)

  ciCovers(x, delta = 0)

  ciOverlap(x, y)

  ciWidth(x)

Arguments

x, y	CIs, as obtained from e.g. the 'acCi' function.
delta	Variant frequency value to check against [default: 0].

Value

A logical vector, where each elements corresponds to the respective row of 'x' (and 'y').

For 'ciWidth': A numeric vector with the widths of the confidence intervals.

Examples

## Generate sample data
counts = data.frame(x1 = 1:5, n1 = 30, x2 = 0:4, n2 = 30)
  
## Agresti-Caffo
ci_ac = with(counts, acCi(x1, n1, x2, n2))
ci_ac2 = with(counts, acCi(x1, n1, x2, n2, 0.99))
  
## cover 0
idx_zero = ciCovers(ci_ac)

## cover 1
idx_one = ciCovers(ci_ac, delta = 1)

## overlap
idx_same = ciOverlap(ci_ac, ci_ac2)

## width
width = ciWidth(ci_ac)

Rariant documentation built on Nov. 8, 2020, 6:56 p.m.