Order/sort genotype/haplotype object
Order/sort genotype or haplotype object according to order of allele names or genotypes
## 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
... |
genotype or haplotype in |
x |
genotype or haplotype in |
na.last |
|
decreasing |
|
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 |
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.
The same as in order or sort
Gregor Gorjanc
genotype,
allele.names,
order, and
sort
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"Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.