Sum multiple variables by group [duplicate]

Answer 1

Plain old aggregate would do:

newdataframe <- aggregate(. ~ gene_id, dataframe, sum)

The formula reads everything else aggregated by gene_id, and sum to compute the sum of all values. You could also use mean for instance.

If you just want some of the other columns, you can cbind them:

newdataframe <- aggregate(cbind(col1, col2) ~ gene_id, dataframe, sum)

Answer 2

Another option:

library(dplyr)
df %>%
  group_by(gene_id) %>%
  summarise_each(funs(sum))

Which gives:

#Source: local data frame [7 x 7]
#
#             gene_id     KOIN1    KOIN2     KOIN3     KOIP1    KOIP2       KOIP3
#              (fctr)     (dbl)    (dbl)     (dbl)     (dbl)    (dbl)       (dbl)
#1 ENSMUSG00000000001 6.0056300 4.677550 6.3490400 9.9992300 9.931780 12.56900000
#2 ENSMUSG00000000003 0.0000000 0.000000 0.0000000 0.0000000 0.000000  0.00000000
#3 ENSMUSG00000000028 0.9988830 0.407537 1.5629300 0.1845460 1.899790  0.85186600
#4 ENSMUSG00000000031 0.0000000 0.818696 0.3708190 0.0419544 0.000000  0.02832700
#5 ENSMUSG00000000037 0.0160579 0.172857 0.0988266 0.0000000 1.174690  0.00726742
#6 ENSMUSG00000000049 0.3923090 0.000000 0.0000000 0.0000000 0.124112  0.01811530
#7 ENSMUSG00000025515 0.6936114 0.134674 1.4382170 0.0000000 0.000000  0.00000000