AGHmatrix (version 2.1.4)

Mcheck: 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
)

Value

SNPmatrix after filtering steps.

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.

Author

Luis F V Ferrao and Rodrigo Amadeu,

Examples

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