CODEWITHSUNDEEP
rmatrixbinary-data
biojl
biojl

Reputation: 1080

How to create a binary matrix from a data.frame?

I have a data.frame with 16 columns. Here's one example row.

    > data[16,]
                      V1              V2              V3                 V4
    16 comp27182_c0_seq4 ENSP00000442096 ENSG00000011143 ENSFCAP00000011376
                       V5                V6                V7                V8
    16 ENSFCAG00000012261 comp48601_c0_seq1 comp19130_c0_seq3 comp22796_c2_seq3
                       V9 V10                V11                V12
    16 comp146901_c0_seq1     comp157916_c0_seq1 comp158124_c0_seq1
                      V13               V14 V15 V16
    16 comp229797_c0_seq1 comp61875_c0_seq2

I'm only interested in columns 1 and 6-16. The first column contains the name I would like to use as a column name in the matrix, 6 to 16 may contain either a string or '' (nothing). I would like to transform this data.frame into a matrix showing 1 or 0, reflecting the content in columns 6-16.

                  V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
comp27182_c0_seq4 1  1  1  1  0  1  1  1  1   0   0

I've trying to use mask without success. I'm sure there's a very easy option out there.

Thanks for any help.

Upvotes: 1

Views: 1284

Answers (2)

biojl
biojl

Reputation: 1080

I slightly modified your code to my exact needs. Now the first column is naming the rows.

a<-do.call(cbind, lapply(c(6:16), 
        function(x) as.numeric(nchar(as.character(data[,x])) > 0)))
rownames(a)<-data[,1]

It works great, thanks!

Upvotes: 0

Ali
Ali

Reputation: 9830

Try this:

do.call(cbind, lapply(c(1,6:16), 
        function(x) as.numeric(nchar(as.character(data[,x])) > 0)))

Upvotes: 4

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