Question

I have a large data frame that Im working with, the first few lines are as follows:

      Assay   Genotype   Sample    Result
1     001        G         1         0
2     001        A         2         1
3     001        G         3         0 
4     001        NA        4         NA
5     002        T         1         0
6     002        G         2         1
7     002        T         3         0 
8     002        T         4         0
9     003        NA        1         N
10    003        G         2         1
11    003        G         3         1 
12    003        T         4         0

In total I’ll be working with 2000 samples and 168 Assays for each sample. For each sample, Id like extract the data in ‘Result’ for each sample to create either a list or data frame that looks something like this:

Sample  Data
   1    00N
   2    111
   3    001
   4    N00

The resulting data frame (or similar preferred data structure) would thus be 2000 rows and 2 columns. The ‘Data’ line would contain 168 characters each one for each ‘Assay’.

Can somebody help me with this problem?

Answer 1

One approach with package plyr and base function paste:

library(plyr)
ddply(dat, "Sample", summarize, Data = paste(Result, collapse = ""))

  Sample Data
1      1  00N
2      2  111
3      3  001
4      4 NA00

EDIT to address question

Probably the easiest way I can think of to change your NA to N is to use gsub on the result of ddply. Note I’m liberally borrowing the very good point provided by @Brian re: ordering. Do that, it’s a good tip!

out <- ddply(dat, "Sample", summarize, Data = paste(Result[order(Assay)], collapse = ""))

Then use gsub

out$Data <- gsub("NA", "N", out$Data)

et voila:

  Sample Data
1      1  00N
2      2  111
3      3  001
4      4  N00