Description Usage Arguments Value Examples
View source: R/ensure_snp_quality.R
ensure_snp_quality
applies quality checks to SNP data
1 2 3 | 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)
|
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 |
missing_value |
Specify the encoding of missing genotypes. |
remove_duplicated |
Logical scalar. Should only unique marker loci be returned? |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | # 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)
|
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