v1=c(1,3,6,9,12)
v2=c(1,0,1,0,1)
v1+v2
## [1] 2 3 7 9 13
v1-v2
## [1] 0 3 5 9 11
v1*v2
## [1] 1 0 6 0 12
v1/v2
## [1] 1 Inf 6 Inf 12
v3=c(0,1,2,3)
v4=c("aa", "bb","cc", "dd")
v5=c("aa", 1,"cc", 2)
str(v3)
## num [1:4] 0 1 2 3
str(v4)
## chr [1:4] "aa" "bb" "cc" "dd"
str(v5)
## chr [1:4] "aa" "1" "cc" "2"
geno1 = c('AA', 'AA', 'AG', 'GG', 'GG')
geno2 = c('AA', 'AA', 'GG', 'GG', 'GG')
A <- cbind(geno1,geno2)
A
## geno1 geno2
## [1,] "AA" "AA"
## [2,] "AA" "AA"
## [3,] "AG" "GG"
## [4,] "GG" "GG"
## [5,] "GG" "GG"
table(A)
## A
## AA AG GG
## 4 1 5
treatment1 <- c(0,1,2,3,4)
treatment2 <- c(0,2,4,6,8)
treatment3 <- c(0,3,6,9,12)
time <- c(0,2,3,6,8)
exper=data.frame(time,treatment1,treatment2,treatment3)
exper
## time treatment1 treatment2 treatment3
## 1 0 0 0 0
## 2 2 1 2 3
## 3 3 2 4 6
## 4 6 3 6 9
## 5 8 4 8 12
plot(exper$time, exper$treatment3)
completeSNP=read.table("23andMe_complete.txt", header = TRUE, sep = "\t")
str(completeSNP$chromosome)
## Factor w/ 25 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
In this case, chromosome is a factor with 25 levels, while in the example data, chromosome is an integer.
table(completeSNP$genotype)
##
## -- A AA AC AG AT C CC CG CT
## 21109 6676 147157 25036 109001 569 7188 173264 1003 108992
## D DD DI G GG GT I II T TT
## 36 157 17 7061 173054 24727 113 685 6643 148126
onlyA=subset(completeSNP, completeSNP$genotype == 'A')
table(onlyA$chromosome)
##
## 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 4 5 6 7 8 9 MT X Y
## 0 0 0 0 0 0 0 732 5782 162