Split intervals (genomic regions) in individual numbers (nucleotides) - r

Question

I would like to transform my data frame df based in regions in point by point (number by number or nucletide by nucleotide) information.
My input df:
start end state freq
100 103 1nT 22
100 103 3nT 34
104 106 1nT 12
104 106 3nT 16
My expected output:
position state freq
100 1nT 22
101 1nT 22
102 1nT 22
103 1nT 22
100 3nT 34
101 3nT 34
102 3nT 34
103 3nT 34
104 1nT 12
105 1nT 12
106 1nT 12
104 3nT 16
105 3nT 16
106 3nT 16
Any ideas? Thank you very much.

Answer 1

Here is a vectorized approach:
# load your data
df <- read.table(textConnection("start end state freq
100 103 1nT 22
100 103 3nT 34
104 106 1nT 12
104 106 3nT 16"), header=TRUE)
# extract number of needed replications
n <- df$end - df$start + 1
# calculate position and replicate state/freq
res <- data.frame(position = rep(df$start - 1, n) + sequence(n),
state = rep(df$state, n),
freq = rep(df$freq, n))
res
# position state freq
# 1 100 1nT 22
# 2 101 1nT 22
# 3 102 1nT 22
# 4 103 1nT 22
# 5 100 3nT 34
# 6 101 3nT 34
# 7 102 3nT 34
# 8 103 3nT 34
# 9 104 1nT 12
# 10 105 1nT 12
# 11 106 1nT 12
# 12 104 3nT 16
# 13 105 3nT 16
# 14 106 3nT 16

Answer 2

Here is one approach....
Build you data
require(data.table)
fakedata <- data.table(start=c(100,100,104,104),
end=c(103,103,106,106),
state=c("1nT","3nT","1nT","3nT"),
freq=c(22,34,12,16))
Perform calculation
fakedata[ , dur := (end-start+1)]
outdata <- fakedata[ , lapply(.SD,function(x) rep(x,dur))]
outdata[ , position := (start-1)+1:.N, by=list(start,end,state)]
And the output
start end state freq dur position
1: 100 103 1nT 22 4 100
2: 100 103 1nT 22 4 101
3: 100 103 1nT 22 4 102
4: 100 103 1nT 22 4 103
5: 100 103 3nT 34 4 100
6: 100 103 3nT 34 4 101
7: 100 103 3nT 34 4 102
8: 100 103 3nT 34 4 103
9: 104 106 1nT 12 3 104
10: 104 106 1nT 12 3 105
11: 104 106 1nT 12 3 106
12: 104 106 3nT 16 3 104
13: 104 106 3nT 16 3 105
14: 104 106 3nT 16 3 106

Answer 3

This can be accomplished with a simple apply command.
Let's build this in sequence:
You want to perform an operation based on every row, so apply by row should be your first thought (or for loop). So we know we want to use apply(data, 1, row.function).
Think of what you would want to do for a single row. You want to repeat state and freq for every number between start and stop.
To get the range of numbers between start and stop we can use the colon operator start:stop.
Now, R will automatically repeat the values in a vector to match the longest vector length when creating a data.frame. So, we can create the piece from a single row like this:
data.frame(position=(row['start']:row['end']), state=row['state'], freq=row['freq'])
Then we want to bind it all together, so we use `do.call('rbind', result).
Putting this all together now, we have:
do.call('rbind',
apply(data, 1, function(row) {
data.frame(position=(row['start']:row['end']),
state=row['state'], freq=row['freq'])
}))
Which will give you what you want. Hopefully this helps teach you how to approach problems like this in the future too!

Answer 4

Here's rough implementation using for loop.
a = t(matrix(c(100, 103, "1nT" , 22,
100, 103 , "3nT" , 34,
104, 106 , "1nT" , 12,
104, 106 , "3nT" , 16), nrow = 4))
a = data.frame(a, stringsAsFactor = F)
colnames(a) = c("start", "end" , "state", "freq")
a$start = as.numeric(as.character(a$start))
a$end = as.numeric(as.character(a$end))
n = dim(a)[1]
res = NULL
for (i in 1:n) {
position = a$start[i]:a$end[i]
state = rep(a$state[i], length(position))
freq = rep(a$freq[i], length(position))
temp = cbind.data.frame(position, state, freq)
res = rbind(res, temp)
}