strataG (version 2.4.905)

as.data.frame.gtypes: Convert gtypes to data.frame or matrix

Description

Create a formatted data.frame or matrix from a '>gtypes object.

Usage

# S4 method for gtypes
as.data.frame(
  x,
  one.col = FALSE,
  sep = "/",
  ids = TRUE,
  strata = TRUE,
  sort.alleles = TRUE,
  coded.snps = FALSE,
  ref.allele = NULL,
  ...
)
# S4 method for gtypes
as.matrix(
  x,
  one.col = FALSE,
  sep = "/",
  ids = TRUE,
  strata = TRUE,
  sort.alleles = TRUE,
  ...
)

Arguments

x

a '>gtypes object.

one.col

logical. If TRUE, then result has one column per locus.

sep

character to use to separate alleles if one.col is TRUE.

ids

logical. include a column for individual identifiers (ids)?

strata

logical. include a column for current statification (strata)?

sort.alleles

logical. for non-haploid objects, should alleles be sorted in genotypes or left in original order? (only takes affect if one.col = TRUE)

coded.snps

return diploid SNPs coded as 0 (reference allele homozygote), 1 (heterozygote), or 2 (alternate allele homozygote). If this is `TRUE`, the data is diploid, and all loci are biallelic, a data frame of coded genotypes will be returned with one column per locus.

ref.allele

an optional vector of reference alleles for each SNP. Only used if `coded.snps = TRUE`. If provided, it must be at least as long as there are biallelic SNPs in g. If named, the names must match those of all loci in g. If set to `NULL` (default) the major allele at each SNP is used as the reference.

...

additional arguments to be passed to or from methods.

Value

A data.frame or matrix with one row per individual.

See Also

df2gtypes as.matrix

Examples

# NOT RUN {
data(msats.g)

# with defaults (alleles in multiple columns, with ids and stratification)
df <- as.data.frame(msats.g)
str(df)

# one column per locus
onecol.df <- as.data.frame(msats.g, one.col = TRUE)
str(onecol.df)

# just the genotypes
genotypes.df <- as.data.frame(msats.g, one.col = TRUE, ids = FALSE, strata = FALSE)
str(genotypes.df)

# as a matrix instead
genotypes.mat <- as.matrix(msats.g)
str(genotypes.mat)

# }

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