mvc2mvs: mvc2mvs

In madoui/metaVaR: Population Genetic Analysis of Multiple Species from Environmental Molecular Data

Description

mvc2mvs selects the mvc being maximum weighted independent set and passing quality filters to generates the mvs.

Usage

mvc2mvs(MVC, minPop = 3, minCov = 8, freq, minVarCov = 8, sd = 2, minVar = 100)

Arguments

MVC	a list of object of class mvc.
minPop	minimum number of population with minCov, set to 3 by default.
minCov	minimum median depth of coverage, set to 8 by default.
freq	allele frequencies in a data.frame
minVarCov	minimum depth of coverage of loci, set to 8 by default.
sd	standard deviation of depth of coverage to select variant, set to 2 by default.
minVar	minimum number of variants in a mvs, set to 100 by default.

Value

a list of objects of class mvs.

Examples

## Not run: 
e = c(5,6)
p = c(5, 10)
MVC = tryParam(e, p , MS5$cov)
MWIS = getMWIS (MVC)
MVS = mvc2mvs (MWIS, freq = MS5$freq, minPop = 3, minCov = 6 , minVarCov = 8, sd = 2, minVar = 100)
## End(Not run)

madoui/metaVaR documentation built on June 6, 2020, 2:09 p.m.