Combining duplicated rows in R and adding new column containing IDs of duplicates

Question

I have a data frame that looks like this:

Chr start   stop    ref alt Hom/het ID  
chr1    5179574 5183384 ref Del Het 719  
chr1    5179574 5184738 ref Del          


        

Answer 1

Some call to aggregate() should do the trick.

Here's an option that collects the ID's in a list object:

(df1 <- aggregate(df[7], df[-7], unique))
#   Chr   start    stop ref alt Hom.het       ID
# 1 chr1 5179574 5183384 ref Del     Het      719
# 2 chr1 5179574 5184738 ref Del     Het 915, 951
# 3 chr1 5336806 5358384 ref Del     Het      376
# 4 chr1 5347979 5358384 ref Del     Het      228

And here's one that collects them in a character vector:

df2 <- aggregate(df[7], df[-7], 
                 FUN = function(X) paste(unique(X), collapse=", "))

Comparing the results of the two options:

str(df1$ID)
# List of 4
#  $ 0: int 719
#  $ 3: int [1:2] 915 951
#  $ 7: int 376
#  $ 8: int 228

str(df2$ID)
# chr [1:4] "719" "915, 951" "376" "228"