filter_aneuploid: Filter aneuploid chromosomes from progeny individuals
In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

filter_aneuploid

R Documentation

Filter aneuploid chromosomes from progeny individuals

Description

Filter aneuploid chromosomes from progeny individuals

Usage

filter_aneuploid(input.data, aneuploid.info, ploidy, rm_missing = TRUE)

Arguments

`input.data`	name of input object (class `mappoly.data`)
`aneuploid.info`	data.frame with ploidy information by chromosome (columns) for each individual in progeny (rows). The chromosome and individuals names must match the ones in the file used as input in mappoly.
`ploidy`	main ploidy
`rm_missing`	remove also genotype information from chromosomes with missing data (NA) in the aneuploid.info file

Value

object of class mappoly.data

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu

Examples

     aneuploid.info <- matrix(4, nrow=tetra.solcap$n.ind, ncol = 12)
     set.seed(8080)
     aneuploid.info[sample(1:length(aneuploid.info), round((4*length(aneuploid.info))/100),0)] <- 3
     aneuploid.info[sample(1:length(aneuploid.info), round((4*length(aneuploid.info))/100),0)] <- 5

     colnames(aneuploid.info) <- paste0(1:12)
     aneuploid.info <- cbind(inds = tetra.solcap$ind.names, aneuploid.info)

     filt.dat <- filter_aneuploid(input.data = tetra.solcap, 
     aneuploid.info = aneuploid.info, ploidy = 4)

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.