R：获取区间内的数字序列，不起作用

Question

I have the following data frame, it contains coordinates and there respective values, these can be at intervals of length 1,2,4,6,8...

chr  start end   meth   cov  
chr1 16136 16136 100.00  1.0 
chr1 16137 16138 100.00  4.0
...
chr2 16139 16142 100.00  4.5
chr2 16243 16246 100.00 10.0
chr2 16247 16250  83.33  6.0
...
chr3 16251 16256  50.0   2.0

What I want to do is to split each interval (,=1,2) in a equal length of two and keep their respective information: for example:

chr1 16136 16136 100.00  1.0    
chr1 16137 16138 100.00  4.0
...
chr1 16139 16140 100.00  4.5
chr1 16141 16142 100.00  4.5
chr1 16243 16244 100.00 10.0
chr1 16245 16246 100.00 10.0
chr1 16247 16248  83.33  6.0
chr1 16249 16250  83.33  6.0
...
chr2 16251 16252  50.0   2.0    
chr2 16253 16254  50.0   2.0
chr2 16255 16256  50.0   2.0

I've received help and the following code is helping, but I'm getting this error when applying seq

Error in seq.default(start, end + 1, 2): 'from' must be of length 1.

Does anyone knows why and how to fix it or another option?

 df %>% filter(end-start >2 ) %>%rowwise() %>% mutate(start2=list(seq(start,end+1,2)))

Answer 1

Here comes a base R solution. First we make it easier for ourselves by defining a function seqr() that creates sequences out of a range of length 2.

seqr <- function(x) seq(x[[1]], x[[2]])

Then – assuming unique columns as in your example – we create row-wise 1:nrow(dat) sequences of start and stop and fill the results row-wise into a two-columned matrix , and cbind it together with the remaining columns exploiting recycling. Result will be rbind ed.

res <- do.call(rbind, 
        lapply(1:nrow(dat), function(i)
          cbind(chr=dat[i, 1],
                matrix(seqr(dat[i, 2:3]), ncol=2, byrow=TRUE, 
                       dimnames=list(NULL, names(dat)[2:3])), 
                dat[i, 4:5], row.names=NULL)))
res
#     chr start   end   meth  cov
# 1  chr1 16136 16136 100.00  1.0
# 2  chr1 16137 16138 100.00  4.0
# 3  chr2 16139 16140 100.00  4.5
# 4  chr2 16141 16142 100.00  4.5
# 5  chr2 16243 16244 100.00 10.0
# 6  chr2 16245 16246 100.00 10.0
# 7  chr2 16247 16248  83.33  6.0
# 8  chr2 16249 16250  83.33  6.0
# 9  chr3 16251 16252  50.00  2.0
# 10 chr3 16253 16254  50.00  2.0
# 11 chr3 16255 16256  50.00  2.0

Data

dat <- structure(list(chr = c("chr1", "chr1", "chr2", "chr2", "chr2", 
"chr3"), start = c(16136L, 16137L, 16139L, 16243L, 16247L, 16251L
), end = c(16136L, 16138L, 16142L, 16246L, 16250L, 16256L), meth = c(100, 
100, 100, 100, 83.33, 50), cov = c(1, 4, 4.5, 10, 6, 2)), row.names = c(NA, 
-6L), class = "data.frame")