filter_missing {mappoly}

Filter missing genotypes

Description

Excludes markers or individuals based on their proportion of missing data.

Usage

filter_missing(
  input.data,
  type = c("marker", "individual"),
  filter.thres = 0.2,
  inter = TRUE
)

Arguments

input.data

an object of class mappoly.data.

type

one of the following options:

1. "marker": filter out markers based on their percentage of missing data (default).

2. "individual": filter out individuals based on their percentage of missing data.

Please notice that removing individuals with certain amount of data can change some marker parameters (such as depth), and can also change the estimated genotypes for other individuals. So, be careful when removing individuals.

filter.thres

maximum percentage of missing data (default = 0.2).

inter

if TRUE, expects user-input to proceed with filtering.

Author(s)

Marcelo Mollinari, [e-mail].

Examples

plot(tetra.solcap)
dat.filt.mrk <- filter_missing(input.data = tetra.solcap,
                               type = "marker",
                               filter.thres = 0.1,
                               inter = TRUE)
plot(dat.filt.mrk)