Question

I am stuck in a small thing. I have a data frame in R like this

chrom exonCount
chr1         3
chr1         4
chr1         5
chr1         5
chr1         9
chr1        10
chr2         7
chr2        11
chr2        13
chr3         7
chr4         7

I just want the output as

chr1        36
chr2        31
chr3         7
chr4         7

I assume the aggregate function can do that but I am lost in usage.

Thanks

Answer 1

I think the plyr package does this the clearest, but using base R

dat <- structure(list(chrom = c("chr1", "chr1", "chr1", "chr1", "chr1", 
"chr1", "chr2", "chr2", "chr2", "chr3", "chr4"), exonCount = c(3L, 
4L, 5L, 5L, 9L, 10L, 7L, 11L, 13L, 7L, 7L)), .Names = c("chrom", 
"exonCount"), class = "data.frame", row.names = c(NA, -11L))

aggregate(data=dat, exonCount ~ chrom, FUN=sum)

  chrom exonCount
1  chr1        36
2  chr2        31
3  chr3         7
4  chr4         7
>