accBic: accBic computes "accuracy" from "inversionList"

In inveRsion: Inversions in genotype data

Description

accBic computes the accuracy of the classification of chromosomes into previously known inverted and non-inverted populations. The classification is obtained from a majority vote of the classifications produced by the trial segment models whose BIC is greater than a given threshold.

Usage

accBic(object, mem, classFile, nsub, npoints, geno, wROI)

Arguments

object	of class inversionList
mem	vector with the numbering of chromosomes known to have the inversion
classFile	an alternative to mem, it passes the file name containing the numbering of chromosomes known to have the inversion.
nsub	total number of subjects (= 2* total number of chromosomes)
npoints	number of BIC threshold between 0 and max (BIC) for which the accuracy is to be computed
geno	whether the accuracy is assessed for inversion genotype or inversion allele (phased data).
wROI	integer indicating the ROI number to be used. The total number of ROIs are the total number of components in the object list.

Value

accuracy

object of class accuracy

Author(s)

Alejandro Caceres [e-mail]

See Also

inversionList, accuracy

Examples

data(invList)
memFile <- system.file("extdata", "mem.txt", package = "inveRsion")
ac <- accBic(invList, classFile = memFile, nsub = 1000, npoints = 10)
plot(ac)

inveRsion documentation built on Nov. 8, 2020, 5:08 p.m.