Mcheck: Check and filter markers

In prmunoz/AGHmatrix: Relationship Matrices for Diploid and Autopolyploid Species

Check and filter markers

Description

This function does different filtering on the marker matrix

Usage

Mcheck(
  SNPmatrix = NULL,
  ploidy = 2,
  missingValue = -9,
  thresh.maf = 0.05,
  thresh.missing = 0.9,
  thresh.htzy = 0,
  impute.method = "mean",
  rmv.mono = TRUE
)

Arguments

SNPmatrix	matrix (n x m), where n is is individual names and m is marker names (coded inside the matrix as 0, 1, 2, ..., ploidy, and, missingValue).
ploidy	data ploidy (an even number between 2 and 20). Default=2.
missingValue	missing value in data. Default=-9.
thresh.maf	minimum allele frequency accepted to each marker. Default=0.05.
thresh.missing	threshold on missing data, SNPs below of this frequency value will be maintained, if equal to 1, no threshold and imputation is considered. Default = 0.50.
thresh.htzy	threshold heterozigosity, remove SNPs below this threshold. Default=0.
impute.method	"mean" to impute the missing data by the mean per marker, "mode" to impute the missing data by the mode per marker, "global.mean" to impute the missing data by the mean across all markers, "global.mode" to impute the missing data my the mode across all marker. Default = "mean".
rmv.mono	if monomorphic markers should be removed. Default=TRUE.

Value

SNPmatrix after filtering steps.

Author(s)

Luis F V Ferrao and Rodrigo Amadeu, [e-mail]

Examples

data(snp.pine)
M = Mcheck(snp.pine)

prmunoz/AGHmatrix documentation built on Oct. 3, 2023, 5:43 p.m.