imputeGenosWithMeanPerPop | R Documentation |
Impute missing SNP genotypes with the mean of the non-missing, population by population.
imputeGenosWithMeanPerPop(
X,
pops,
min.maf.pop = 0.1,
max.miss.pop = 0.3,
rm.still.miss = TRUE,
verbose = 1
)
X |
matrix of bi-allelic SNP genotypes encoded in allele doses in 0,1,2, with genotypes in rows and SNPs in columns; missing values should be encoded as NA |
pops |
data.frame with 2 columns, "ind" and "pop" |
min.maf.pop |
minimum minor allele frequency per population (before imputation) below which SNPs are discarded |
max.miss.pop |
maximum amount of missing genotypes per population (before imputation) above which SNPs are discarded |
rm.still.miss |
if TRUE, remove SNP(s) still with missing genotype(s) in at least one population (depending on |
verbose |
verbosity level (0/1) |
matrix with imputed genotypes
Timothee Flutre
imputeGenosWithMean
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