mappoly (version 0.4.1)

filter_aneuploid: Filter aneuploid chromosomes from progeny individuals

Description

Filter aneuploid chromosomes from progeny individuals

Usage

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

Value

object of class mappoly.data

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

Author

Cristiane Taniguti,

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)