Description Usage Arguments Details Value Author(s) See Also Examples
This function adds new markers to the element geno
of an object of class gpData
and updates the marker map.
1 | add.markers(gpData, geno, map)
|
gpData |
object of class |
geno |
|
map |
|
rownames
in argument geno
must match rownames
in the element geno
object of class gpData
.
object of class gpData
with new markers
Valentin Wimmer
add.individuals
, discard.markers
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # creating gpData object
# phenotypic data
pheno <- data.frame(Yield = rnorm(10,100,5), Height = rnorm(10,10,1))
rownames(pheno) <- 1:10
# genotypic data
geno <- matrix(sample(c(1,0,2,NA),size=120,replace=TRUE,
prob=c(0.6,0.2,0.1,0.1)),nrow=10)
rownames(geno) <- 1:10
# genetic map
map <- data.frame(chr=rep(1:3,each=4),pos=rep(1:12))
colnames(geno) <- rownames(map) <- paste("M",1:12,sep="")
# as gpData object
gp <- create.gpData(pheno,geno,map)
# new data
geno2 <- matrix(c(0,0,1,1,1,2,2,1,1,2,1,2,0,2,1,1,1,2,2,2),ncol=2)
rownames(geno2) <- 1:10
map2 <- data.frame(pos=c(0.3,5),chr=c(1,2))
rownames(map2) <- colnames(geno2) <- c("M13","M14")
# adding new markers
gp2 <- add.markers(gp,geno2,map2)
summary(gp2)
summary(gp)
|
sh: 1: cannot create /dev/null: Permission denied
object of class 'gpData'
covar
No. of individuals 10
phenotyped 10
genotyped 10
pheno
No. of traits: 2
Yield Height
Min. : 93.22 Min. : 8.020
1st Qu.: 98.72 1st Qu.: 9.109
Median :101.43 Median :10.670
Mean :101.54 Mean :10.171
3rd Qu.:104.40 3rd Qu.:11.024
Max. :108.91 Max. :11.692
geno
No. of markers 14
genotypes 0 1 2
frequencies 0.1785714 0.5642857 0.15
NA's 10.714 %
map
No. of mapped markers 14
No. of chromosomes 3
markers per chromosome
1 2 3
5 5 4
pedigree
NULL
object of class 'gpData'
covar
No. of individuals 10
phenotyped 10
genotyped 10
pheno
No. of traits: 2
Yield Height
Min. : 93.22 Min. : 8.020
1st Qu.: 98.72 1st Qu.: 9.109
Median :101.43 Median :10.670
Mean :101.54 Mean :10.171
3rd Qu.:104.40 3rd Qu.:11.024
Max. :108.91 Max. :11.692
geno
No. of markers 12
genotypes 0 1 2
frequencies 0.1833333 0.5833333 0.1083333
NA's 12.500 %
map
No. of mapped markers 12
No. of chromosomes 3
markers per chromosome
1 2 3
4 4 4
pedigree
NULL
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