library(genetics) suppressWarnings(RNGversion("3.5.0")) set.seed(12345) # 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 <- makeGenotypes(test1) geno1 set.seed(12345) # Create a test data set where there are several genotypes in columns # of the form "A_T". test1.b <- 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) ) # now automatically convert genotype columns geno1.b <- makeGenotypes(test1.b, sep="_") stopifnot(identical(geno1,geno1.b))
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