Consider the data frame below. I want to compare each row with rows below and then take the rows that are equal in more than 3 values.
I wrote the code below, but it is very slow if you have a large data frame.
How could I do that faster?
data <- as.data.frame(matrix(c(10,11,10,13,9,10,11,10,14,9,10,10,8,12,9,10,11,10,13,9,13,13,10,13,9), nrow=5, byrow=T))
rownames(data)<-c("sample_1","sample_2","sample_3","sample_4","sample_5")
>data
V1 V2 V3 V4 V5
sample_1 10 11 10 13 9
sample_2 10 11 10 14 9
sample_3 10 10 8 12 9
sample_4 10 11 10 13 9
sample_5 13 13 10 13 9
tab <- data.frame(sample = NA, duplicate = NA, matches = NA)
dfrow <- 1
for(i in 1:nrow(data)) {
sample <- data[i, ]
for(j in (i+1):nrow(data)) if(i+1 <= nrow(data)) {
matches <- 0
for(V in 1:ncol(data)) {
if(data[j,V] == sample[,V]) {
matches <- matches + 1
}
}
if(matches > 3) {
duplicate <- data[j, ]
pair <- cbind(rownames(sample), rownames(duplicate), matches)
tab[dfrow, ] <- pair
dfrow <- dfrow + 1
}
}
}
>tab
sample duplicate matches
1 sample_1 sample_2 4
2 sample_1 sample_4 5
3 sample_2 sample_4 4
