GenoCod_Gen: Transforms the genetic maker

In CroteauCRIUSMQ/EMQLS.test: Extension of MQLS test

Description

Function transforms the genetic marker to recessive, dominant or codominant mode.

Usage

GenoCod_Gen(data, MA, genotyp, Method, var.nam = NULL, na.rm = FALSE)

Arguments

data	Data frame of the database
MA	Minor allele name in the database
genotyp	Genotype name in the database
Method	The method to useMethod = c("recessive", "dominant", "codominant")
var.nam	Name of the new variable, by default the name is X2
na.rm	TRUE, the function conserves the missing data and FALSE, it suppresses the individuals, which have the missing data.

Details

Function that transforms the genetic marker according to the mode ("recessive", "dominant", "co-dominant") and assess the allele minor frequency under Hardy Weinberg equilibrium of the target population.

Value

Return a list containing

datR	Data frame with the new variable
MA.frq	Minor allele frequency

Note

We use the documentation of the site below to code the genetic markers in "Dominant", "Recessive" and "codominant" mode.

References

http://wims.unice.fr/wims/wims.cgi?module=U1/genetics/docpopulation.fr

Examples

# Example : Genotype data

  set.seed(123000)
  snp1 <- c("aaAA","AA:aA","Aa/AA","aa/AA","aA/aa","Aa/Aa","AA/Aa","AA/Aa","AA/Aa",NA)
  snp2 <- c("Aa/aA","Aa/AA","AA/aa","AA/aA","AA/Aa","Aa,AA","AA/AA","AA/aA","Aa/aa","")
  datD<-NULL
  for(u in 1:10){
              SNP1<-sample(snp1)
              SNP2<-sample(snp2)
              var1 <- runif(length(snp1))
              pheno<- rbinom(length(snp1),c(0,1),prob=c(0.65,0.35))
              pheno[sample(1:length(snp1))[3]]<-NA
              id<-c(1:length(snp1))
              id.fam<-rep(u,length(snp1))
              tabGen1<-data.frame(id.fam,id,SNP1,SNP2,var1,pheno)
              datD<-rbind(datD,tabGen1)
              }
  # Result
    head(datD)
    
  # Example of the using GenoCod_Gen
  # 'a' is the minor allele, method "recessive" the new name is X2
   datT1<-GenoCod_Gen(datD,"a","SNP2",Method=c("recessive"),var.nam="X2")
   head(datT1$datR)

CroteauCRIUSMQ/EMQLS.test documentation built on May 6, 2019, 12:52 p.m.