ensure_snp_quality: Ensure SNP Quality

In mwesthues/sspredr: Single-Step Prediction

Description

ensure_snp_quality applies quality checks to SNP data

Usage

ensure_snp_quality(snp, callfreq_check = TRUE, callfreq_threshold = 0.95,
  maf_check = TRUE, maf_threshold = 0.05, any_missing = TRUE,
  missing_value = NA_character_, remove_duplicated = TRUE)

Arguments

snp	A matrix. Genotype names are stored in rows whereas marker names are stored in columns.
callfreq_check	Logical scalar. Shall markers with a low call frequency (*i.e.* a high number of missing marker genotypes) be removed?
callfreq_threshold	Numeric scalar. Minimum level of non-missing genotypes per locus.
maf_check	Logical scalar. Shall markers with a low minor allele frequency be removed?
maf_threshold	Numeric scalar. Minimum frequency of the minor allele at each locus.
any_missing	Logical scalar. Does the input matrix snp contain any missing values? If this is the case, they will be replaced with the major genotype at this locus.
missing_value	Specify the encoding of missing genotypes.
remove_duplicated	Logical scalar. Should only unique marker loci be returned?

Value

Depending on the choice of parameters callfreq_check and maf_check, respectively, ensure_snp_quality will return a matrix with marker genotypes that have passed important quality checks.

Examples

 # Load a matrix with SNP genotypes encoded as numeric values
 data(marker_numeric)

 # Add a duplicated marker locus to the data.
 snp <- marker_numeric
 snp <- cbind(snp, snp[, 1])

 # Return markers without missing values, a call frequency greater or equal
 # to 0.95 and a minor allele frequency greater or equal to 0.6. Finally,
 # remove all duplicated markers.
 ensure_snp_quality(snp, maf_threshold = 0.1, missing_value = NA_real_)

 # Load a matrix with SNP genotypes encoded as character values
 data(marker_character)

 # Return markers without missing values and a call frequency equal to or
 # greater than 0.9. Keep duplicated markers if present.
 ensure_snp_quality(marker_character, callfreq_threshold = 0.9,
                    maf_check = FALSE, missing_value = "??",
                    remove_duplicated = FALSE)

mwesthues/sspredr documentation built on May 23, 2019, 10:56 a.m.