Concatenate several columns to comma separated strings by group

by

You could do this in one line using plyr, as it is a classic split-apply-combine problem. You split using SNP, apply paste with collapse and assemble the pieces back into a data frame. 

plyr::ddply(x, .(SNP), colwise(paste), collapse = ",")

If you want to do data reshaping in R at the flick of a wrist, learn plyr and reshape2 :). Another flick of the wrist solution using data.table, really useful if you are dealing with massive amounts of data.

data.table::data.table(x)[,lapply(.SD, paste, collapse = ","),'SNP']

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