as.geneSet {GeneticsBase}R Documentation

Convert an existing object to a geneSet

Description

Convert an existing object to a geneSet. Methods currenrly exist only for matrix and data.frame objects.

Usage

## S3 method for class 'matrix':
as.geneSet(x, ... )
## S3 method for class 'data.frame':
as.geneSet(x,
  gene.columns,
  format=c("single", "adjacent"),
  ploidy=2,
  alleles=NULL,
  sep="/",
  remove.spaces=TRUE,
  reorder=c("freq", "yes", "no", "default", "ascii"),
  allow.partial.missing=FALSE,
  markerNames,
  phase=list(F),
  ...)

Arguments

x The matrix or data.frame object to be converted
gene.columns Names or indexes of columns containing genotypes
format One of "single", indiciating that each specified column contains a complete genotype (e.g. "A/C"), or "adjacent" indicating that sets of ploidy adjacent columns each contain as single allele (e.g. "A", "C")
ploidy Number of allele copies per genotype. Defaults to 2
alleles Not currently supported. In the future, this variable will allow specification of the allele strings for each genotype.
sep A character value or a numeric index vector indicating how allels are spearated within genotypes, defaults to "/". If a character, it indicates that alleles within a genotype are separated by this character (e.g. for "A/C", sep="/"). If a numeric vector (of length ploidy-1), the value(s) indicate which positions separate allele names (e.g. for "AA", sep=1).
remove.spaces Should whitespace be removed before processing.
reorder One of "freq", "yes", "no", "default", or "ascii", indicating whether and how alleles should be reorderd within genotypes.
If reorder="no", the observed order is preserved (important when phase is known).
If reorder="freq", sort alleles within each individual by observed frequency.
If reorder="yes", sort alleles in the order provided by the alleles argument.
If reorder="ascii", reorder alleles in ASCII order (alphabetical, with all upper case before lower case).
The default value is "freq".
allow.partial.missing Logical value indicating whether a genotype is permitted to be partially missing. When allow.partial.missing=FALSE, if any individual allele is missing within a genotype, the entire genotype will be converted to a missing value. When allow.partial.missing=TRUE, the missingness of individual alleles will be preserved.
markerNames Character vector of names to use for the genotype columns. This must have the same lenght as the number of genotype columns.
phase List indicating whether phase is known for each genotype column. If the list has a single logical entry, this will apply to all genotype columns.
... Optional arguments.

Value

An S4 object of class geneSet

Author(s)

Gregory R. Warnes greg@random-technologies-llc.com

See Also

geneSet

Examples


## Create a test data set where there are several genotypes in columns
## of the form "A/T".
test1 <- data.frame(Tmt=sample(c("Control","Trt1","Trt2"),20, replace=TRUE),
                G1=sample(c("A/T","T/T","T/A",NA),20, replace=TRUE),
                N1=rnorm(20),
                I1=sample(1:100,20,replace=TRUE),
                G2=paste(sample(c("134","138","140","142","146"),20,
                                replace=TRUE),
                         sample(c("134","138","140","142","146"),20,
                                replace=TRUE),
                         sep=" / "),
                G3=sample(c("A /T","T /T","T /A"),20, replace=TRUE),
                comment=sample(c("Possible Bad Data/Lab Error",""),20,
                               rep=TRUE)
                )
test1

## now automatically convert genotype columns
geno1 <- as.geneSet(test1)
geno1


[Package GeneticsBase version 1.8.0 Index]