order.genotype: Order/sort genotype/haplotype object

In kindlychung/genetics: Population Genetics

Description

Order/sort genotype or haplotype object according to order of allele names or genotypes

Usage

## S3 method for class 'genotype'
order(..., na.last=TRUE, decreasing=FALSE,
  alleleOrder=allele.names(x), genotypeOrder=NULL)

## S3 method for class 'genotype'
sort(x, decreasing=FALSE, na.last=NA, ...,
  alleleOrder=allele.names(x), genotypeOrder=NULL)

genotypeOrder(x)
genotypeOrder(x) <- value

Arguments

...	genotype or haplotype in order method; not used for sort method
x	genotype or haplotype in sort method
na.last	as in default order or sort
decreasing	as in default order or sort
alleleOrder	character, vector of allele names in wanted order
genotypeOrder	character, vector of genotype/haplotype names in wanted order
value	the same as in argument order.genotype

Details

Argument genotypeOrder can be usefull, when you want that some genotypes appear "together", whereas they are not "together" by allele order.

Both methods (order and sort) work with genotype and haplotype classes.

If alleleOrder is given, genotypeOrder has no effect.

Genotypes/haplotypes, with missing alleles in alleleOrder are treated as NA and ordered according to order arguments related to NA values. In such cases a warning is issued ("Found data values not matching specified alleles. Converting to NA.") and can be safely ignored. Genotypes present in x, but not specified in genotypeOrder, are also treated as NA.

Value of genotypeOrder such as "B/A" matches also "A/B" in case of genotypes.

Only unique values in argument alleleOrder or genotypeOrder are used i.e. first occurrence prevails.

Value

The same as in order or sort

Author(s)

Gregor Gorjanc

See Also

genotype, allele.names, order, and sort

Examples

  x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B", "B/C", "A/C")
  alleles <- c("A", "B", "C")

  g <- genotype(x, alleles=alleles, reorder="yes")
  ## "C/C" "A/C" "A/A" NA    "B/C" "A/B" "B/B" "B/C" "A/C"

  h <- haplotype(x, alleles=alleles)
  ## "C/C" "A/C" "A/A" NA    "C/B" "B/A" "B/B" "B/C" "A/C"

  ## --- Standard usage ---

  sort(g)
  ## "A/A" "A/B" "A/C" "A/C" "B/B" "B/C" "B/C" "C/C" NA

  sort(h)
  ## "A/A" "A/C" "A/C" "B/A" "B/B" "B/C" "C/B" "C/C" NA

  ## --- Reversed order of alleles ---

  sort(g, alleleOrder=c("B", "C", "A"))
  ## "B/B" "B/C" "B/C" "A/B" "C/C" "A/C" "A/C" "A/A" NA
  ## note that A/B comes after B/C since it is treated as B/A;
  ## order of alleles (not in alleleOrder!) does not matter for a genotype

  sort(h, alleleOrder=c("B", "C", "A"))
  ## "B/B" "B/C" "B/A" "C/B" "C/C" "A/C" "A/C" "A/A" NA

  ## --- Missing allele(s) in alleleOrder ---

  sort(g, alleleOrder=c("B", "C"))
  ## "B/B" "B/C" "B/C" "C/C" "A/C" "A/A" NA    "A/B" "A/C"

  sort(g, alleleOrder=c("B"))
  ## "B/B" "C/C" "A/C" "A/A" NA    "B/C" "A/B" "B/C" "A/C"
  ## genotypes with missing allele are treated as NA

  sort(h, alleleOrder=c("B", "C"))
  ## "B/B" "B/C" "C/B" "C/C" "A/C" "A/A" NA    "B/A" "A/C"

  sort(h, alleleOrder=c("B"))
  ## "B/B" "C/C" "A/C" "A/A" NA    "C/B" "B/A" "B/C" "A/C"

  ## --- Use of genotypeOrder ---

  sort(g, genotypeOrder=c("A/A", "C/C", "B/B", "A/B", "A/C", "B/C"))
  ## "A/A" "C/C" "B/B" "A/B" "A/C" "A/C" "B/C" "B/C" NA

  sort(h, genotypeOrder=c("A/A", "C/C", "B/B",
                          "A/C", "C/B", "B/A", "B/C"))
  ## "A/A" "C/C" "B/B" "A/C" "A/C" "C/B" "B/A" "B/C" NA

  ## --- Missing genotype(s) in genotypeOrder ---

  sort(g, genotypeOrder=c(       "C/C",        "A/B", "A/C", "B/C"))
  ## "C/C" "A/B" "A/C" "A/C" "B/C" "B/C" "A/A" NA    "B/B"

  sort(h, genotypeOrder=c(       "C/C",        "A/B", "A/C", "B/C"))
  ## "C/C" "A/C" "A/C" "B/C" "A/A" NA    "C/B" "B/A" "B/B"

kindlychung/genetics documentation built on May 20, 2019, 9:58 a.m.