filter_missing {onemap}

Filter markers according with a missing data threshold

Description

Filter markers according with a missing data threshold

Usage

filter_missing(
  onemap.obj = NULL,
  threshold = 0.25,
  by = "markers",
  verbose = TRUE
)

Arguments

onemap.obj

an object of class onemap.

threshold

a numeric from 0 to 1 to define the threshold of missing data allowed

by

character defining if 'markers' or 'individuals' should be filtered

verbose

A logical, if TRUE it output progress status information.

Value

An object of class onemap, i.e., a list with the following components:

geno

a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.

n.ind

number of individuals.

n.mar

number of markers.

segr.type

a vector with the segregation type of each marker, as strings.

segr.type.num

a vector with the segregation type of each marker, represented in a simplified manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corresponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6 corresponds to markers of type "D1" and 7 corresponds to markers of type "D2". Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.

input

the name of the input file.

n.phe

number of phenotypes.

pheno

a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.

error

matrix containing HMM emission probabilities

Author(s)

Cristiane Taniguti, [e-mail]

Examples

  data(onemap_example_out)
  filt_obj <- filter_missing(onemap_example_out, threshold=0.25)