create a loop and paste

Question

I am having a problem with a loop. I have a data frame:

Transcript=c(1,1,1,1,2,2,2,2,2)
Exon=rep(c(1:4,1:5))
S=c("aaa","ttt","ccc","ggg","ata","tat","cgc","gcg","bbb")
E=c("AAA","TTT","CCC","GGG","ATA","TAT","CGC","GCG","BBB")
DF=data.frame(Transcript, Exon, S, E)
DF
s=split( DF , DF$Transcript,)

I want to subset the dataframe by Transcript and paste column E with S together to give all possible combinations in each transcript. For example, for Transcript 1, I want to return:

AAAaaa,AAAttt,AAAccc,AAAggg,TTTaaa,TTTttt,TTTccc,TTTggg,CCCaaa,CCCttt,CCCccc,CCCggg,GGGaaa,GGGttt,GGGccc,GGGggg.

I have tried the following loop, but it only returns the AAAaaa AAAttt AAAccc AAAggg:

for(i in 1:nrow(s[[1]])){p=paste(s[[1]][1,4],s[[1]][1:i,3],sep="")}

How to I create this loop?

Vincent Guillemot · Accepted Answer · 2014-11-26 12:32:32Z

2

Something like this might work:

lapply(s, function(df) apply(expand.grid(df$E, df$S),1,paste0,collapse=""))

Or, as proposed by @akrun,

lapply(s, function(df) do.call(paste0, expand.grid(df$E, df$S)))

edited Nov 26, 2014 at 12:32

answered Nov 26, 2014 at 11:19

Vincent Guillemot

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2 Comments

biobirdman Over a year ago

Good use of expand.grid!

akrun Over a year ago

You could also do lapply(s, function(df) do.call(paste0, expand.grid(df$E, df$S)))

akrun · Accepted Answer · 2014-11-26 11:24:14Z

1

You could try data.table

library(data.table)
setDT(DF)[,Reduce(paste0,CJ(E, S)), by=Transcript]

data

DF <- data.frame(Transcript, Exon, S, E)

answered Nov 26, 2014 at 11:24

akrun

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