groupGenotype: Group genotype values

In kindlychung/genetics: Population Genetics

Description

groupGenotype groups genotype or haplotype values according to given "grouping/mapping" information

Usage

groupGenotype(x, map, haplotype=FALSE, factor=TRUE, levels=NULL, verbose=FALSE)

Arguments

x	genotype or haplotype
map	list, mapping information, see details and examples
haplotype	logical, should values in a map be treated as haplotypes or genotypes, see details
factor	logical, should output be a factor or a character
levels	character, optional vector of level names if factor is produced (factor=TRUE); the default is to use the sort order of the group names in map
verbose	logical, print genotype names that match entries in the map - mainly used for debugging

Details

Examples show how map can be constructed. This are the main points to be aware of:

• names of list components are used as new group names

• list components hold genotype names per each group

• genotype names can be specified directly i.e. "A/B" or abbreviated such as "A/*" or even "*/*", where "*" matches any possible allele, but read also further on

• all genotype names that are not specified can be captured with ".else" (note the dot!)

• genotype names that were not specified (and ".else" was not used) are changed to NA

map is inspected before grouping of genotypes is being done. The following steps are done during inspection:

• ".else" must be at the end (if not, it is moved) to match everything that has not yet been defined

• any specifications like "A/*", "*/A", or "*/*" are extended to all possible genotypes based on alleles in argument alleles - in case of haplotype=FALSE, "A/*" and "*/A" match the same genotypes

• since use of "*" and ".else" can cause duplicates along the whole map, duplicates are removed sequentially (first occurrence is kept)

Using ".else" or "*/*" at the end of the map produces the same result, due to removing duplicates sequentially.

Value

A factor or character vector with genotypes grouped

Author(s)

Gregor Gorjanc

See Also

genotype, haplotype, factor, and levels

Examples

## --- Setup ---

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

h <- haplotype(x)
## "A/A" "A/B" "B/A" "A/C" "C/A" "A/D" "D/A" "B/B" "B/C" "C/B" "B/D" "D/B"
## "C/C" "C/D" "D/C" "D/D"

## --- Use of "A/A", "A/*" and ".else" ---

map <- list("homoG"=c("A/A", "B/B", "C/C", "D/D"),
            "heteroA*"=c("A/B", "A/C", "A/D"),
            "heteroB*"=c("B/*"),
            "heteroRest"=".else")

(tmpG <- groupGenotype(x=g, map=map, factor=FALSE))
(tmpH <- groupGenotype(x=h, map=map, factor=FALSE, haplotype=TRUE))

## Show difference between genotype and haplotype treatment
cbind(as.character(h), gen=tmpG, hap=tmpH, diff=!(tmpG == tmpH))
##              gen          hap          diff
##  [1,] "A/A" "homoG"      "homoG"      "FALSE"
##  [2,] "A/B" "heteroA*"   "heteroA*"   "FALSE"
##  [3,] "B/A" "heteroA*"   "heteroB*"   "TRUE"
##  [4,] "A/C" "heteroA*"   "heteroA*"   "FALSE"
##  [5,] "C/A" "heteroA*"   "heteroRest" "TRUE"
##  [6,] "A/D" "heteroA*"   "heteroA*"   "FALSE"
##  [7,] "D/A" "heteroA*"   "heteroRest" "TRUE"
##  [8,] "B/B" "homoG"      "homoG"      "FALSE"
##  [9,] "B/C" "heteroB*"   "heteroB*"   "FALSE"
## [10,] "C/B" "heteroB*"   "heteroRest" "TRUE"
## [11,] "B/D" "heteroB*"   "heteroB*"   "FALSE"
## [12,] "D/B" "heteroB*"   "heteroRest" "TRUE"
## [13,] "C/C" "homoG"      "homoG"      "FALSE"
## [14,] "C/D" "heteroRest" "heteroRest" "FALSE"
## [15,] "D/C" "heteroRest" "heteroRest" "FALSE"
## [16,] "D/D" "homoG"      "homoG"      "FALSE"

map <- list("withA"="A/*", "rest"=".else")
groupGenotype(x=g, map=map, factor=FALSE)
##  [1] "withA" "withA" "withA" "withA" "withA" "withA" "withA" "rest"  "rest"
## [10] "rest"  "rest"  "rest"  "rest"  "rest"  "rest"  "rest"

groupGenotype(x=h, map=map, factor=FALSE, haplotype=TRUE)
##  [1] "withA" "withA" "rest"  "withA" "rest"  "withA" "rest"  "rest"  "rest"
## [10] "rest"  "rest"  "rest"  "rest"  "rest"  "rest"  "rest"

## --- Use of "*/*" ---

map <- list("withA"="A/*", withB="*/*")
groupGenotype(x=g, map=map, factor=FALSE)
##  [1] "withA" "withA" "withA" "withA" "withA" "withA" "withA" "withB" "withB"
## [10] "withB" "withB" "withB" "withB" "withB" "withB" "withB"

## --- Missing genotype specifications produces NA's ---

map <- list("withA"="A/*", withB="B/*")
groupGenotype(x=g, map=map, factor=FALSE)
##  [1] "withA" "withA" "withA" "withA" "withA" "withA" "withA" "withB" "withB"
## [10] "withB" "withB" "withB" NA      NA      NA      NA

groupGenotype(x=h, map=map, factor=FALSE, haplotype=TRUE)
##  [1] "withA" "withA" "withB" "withA" NA      "withA" NA      "withB" "withB"
## [10] NA      "withB" NA      NA      NA      NA      NA

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