Convert geno slot from SNPDataLong to a data.frame

Converts the genotype matrix (geno slot) of a SNPDataLong object to a data.frame, with optional centering and scaling per SNP (column).

genoToDF(object, center = FALSE, scale = FALSE)

Arguments

object: An object of class SNPDataLong.
center: Logical or numeric. If TRUE (default FALSE), center columns to mean zero.
scale: Logical or numeric. If TRUE (default FALSE), scale columns to standard deviation one.

Value

A data.frame with individuals as rows and SNPs as columns (numeric 0/1/2, or centered/scaled values).

Examples

# \donttest{
set.seed(1)
raw_mat <- matrix(as.raw(sample(1:3, 100, TRUE)), nrow = 10, ncol = 10)
rownames(raw_mat) <- paste0("S", 1:10)
colnames(raw_mat) <- paste0("SNP", 1:10)
geno <- methods::new("SnpMatrix", raw_mat)
obj <- methods::new("SNPDataLong",
                    geno = geno,
                    map  = data.frame(Name = colnames(geno),
                                      Chromosome = 1,
                                      Position = 1:10),
                    path = tempfile(),
                    xref_path = "chip1")
df <- genoToDF(obj, center = TRUE, scale = TRUE)
#> No monomorphic SNPs detected. Skipping subset.
#> Applying centering and/or scaling to SNP columns...
#> Genotype data converted to data.frame with dimensions: 10 x 10
head(df[, 1:5])
#>         SNP1       SNP2       SNP3       SNP4      SNP5
#> S1 -1.256289  1.5212777  2.1213203 -0.1355262  0.000000
#> S2  1.027872 -1.0141851 -0.7071068 -1.4907880 -1.224745
#> S3 -1.256289 -1.0141851 -0.7071068  1.2197357  1.224745
#> S4 -0.114208 -1.0141851 -0.7071068 -1.4907880  0.000000
#> S5 -1.256289  0.2535463 -0.7071068  1.2197357 -1.224745
#> S6  1.027872  0.2535463  0.7071068 -0.1355262 -1.224745
# }