as.genalex: Convert object to class genalex

In douglasgscofield/readGenalex: Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files

Description

Converts object x to a data frame of class genalex. There are seven cases:

• If x is of class genalex, it is simply returned.

• If x is of class genalex and force = TRUE, x is examined for consistency between data and annotations, and any inconsistencies are recalculated based on the data. To check whether inconsistencies exist, use is.genalex(..., force = TRUE) and add verbose = TRUE for descriptions of the inconsistencies. Ploidy is taken from x and is not reset. Attributes that may be reset include n.samples, sample.title, n.loci, locus.columns, locus.names, n.pops, pop.labels, pop.sizes and pop.title.

• If x is of class 'data.frame', it is examined to see if it might be a data frame created by an earlier version of the readGenalex package. If so, it is converted to class genalex and returned. Any other arguments are ignored.

• If x is of class 'data.frame' and all columns from the third to the end are of class genotype from the genetics package, these columns are converted to class genalex genotypes, with one column per allele. Once the alleles have been split, a call to genalex establishes the correct attributes.

• If x is of class 'data.frame' but does not appear to be from an earlier version of readGenalex and does not have all genotype columns of class genotype, it is converted to class genalex using a call to genalex assuming a format identical to class genalex, where the first column holds sample names, the second column holds population names, and the remaining columns hold genotypes.

• If x is of class loci from the pegas package, it is converted using splitGenotypes and genalex. Sample names are taken from the row names. If there is no column in x named "population", then the pop argument must be supplied as a substitute. Additional non-genotype columns will likely result in an error. No attempt is currently made to use the "locicol" attribute to narrow the conversion to only locus columns. Furthermore, only diploid genotypes are currently handled.

• Any other class is an error. Further conversions between genetic data formats may be added as additional methods.

If the object is not originally of class genalex, the "data.file.name" attribute will reflect this function call.

Usage

## S3 method for class 'genalex'
as.genalex(x, force = FALSE, ...)

## S3 method for class 'data.frame'
as.genalex(x, names = NULL, ploidy = 2, ...)

## S3 method for class 'loci'
as.genalex(x, sep = "/", pop, ...)

## Default S3 method:
as.genalex(x, ...)

Arguments

x	An object of class genalex or class 'data.frame'
force	If TRUE, check for consistency between data and annotations in x and recalculate and reset any inconsistent attributes. This option is only used if x has class genalex, and is FALSE by default.
names	A list of names to apply as accepted by genalex. If any names are not provided, they are taken from the names of the corresponding columns of x. This option is only used if x does not have class genalex.
ploidy	Ploidy of the genotype columns in x (x[, 3:ncol(x)]). This option is only used if x does not have class genalex.
sep	Character separating joined alleles, if converting from object of class 'loci'
pop	Populations to assign to samples if there is no population column in the data
...	Additional arguments, ignored unless x is of class 'loci' and if so passed to genalex

Value

x converted to a class genalex object

Author(s)

Douglas G. Scofield

See Also

is.genalex, genalex, splitGenotypes

Examples

data(Qagr_adult_genotypes)
gt <- as.genalex(Qagr_adult_genotypes)
cat(attr(gt, "data.file.name"), "\n")
gt.2 <- as.genalex(as.data.frame(Qagr_adult_genotypes))
cat(attr(gt.2, "data.file.name"), "\n")

douglasgscofield/readGenalex documentation built on May 15, 2019, 10:43 a.m.