[R] data frame pointers?

arun smartpink111 at yahoo.com
Thu Oct 24 05:04:51 CEST 2013

Hi Jonathan,If you look at the str()
'data.frame':    2 obs. of  4 variables:
 $ gene  : chr  "gene1" "gene2"
 $ case_1:List of 2
  ..$ : chr  "nsyn" "amp"
  ..$ : chr 
 $ case_2:List of 2
  ..$ : chr "del"
  ..$ : chr 
 $ case_3:List of 2
  ..$ : chr 
  ..$ : chr "UTR"

In this case, 

capture.output(res,file="test.txt") #should work

But, if you wanted to use ?write.table() and also to substitute zeros, perhaps:

res[,2:4] <- lapply(res[,2:4],function(x) {x1 <-unlist(lapply(x,paste,collapse=","));x1[x1==""] <- 0; x1})

#'data.frame':    2 obs. of  4 variables:
# $ gene  : chr  "gene1" "gene2"
# $ case_1: chr  "nsyn,amp" "0"
# $ case_2: chr  "del" "0"
# $ case_3: chr  "0" "UTR"



On Wednesday, October 23, 2013 10:44 PM, Jon BR <jonsleepy at gmail.com> wrote:

Hi Arun,
   Your suggestion using dcast is simple and worked splendidly!  Unfortunately, the resulting data frame does not play nicely with write.table.

Any idea how to could print this out to a tab-delimited text file, perhaps substituting zeros in for the empty cells?

See the error below:
> write.table(res,"test.txt")
Error in .External2(C_writetable, x, file, nrow(x), p, rnames, sep, eol,  : 
  unimplemented type 'list' in 'EncodeElement'


On Wed, Oct 23, 2013 at 9:50 PM, arun <smartpink111 at yahoo.com> wrote:

>You may try:
>df <-
>data.frame(case=c("case_1","case_1","case_2","case_3"), gene=c("gene1","gene1","gene1","gene2"), issue=c("nsyn","amp","del","UTR"), stringsAsFactors=FALSE)
>res <- dcast(df,gene~case,value.var="issue",list)
> res
>#   gene    case_1 case_2 case_3
>#1 gene1 nsyn, amp    del      
>#2 gene2                     UTR
>On Wednesday, October 23, 2013 7:38 PM, Jon BR <jonsleepy at gmail.com> wrote:
>    I've been running several programs in the unix shell, and it's time to
>combine results from several different pipelines.  I've been writing shell
>scripts with heavy use of awk and grep to make big text files, but I'm
>thinking it would be better to have all my data in one big structure in R
>so that I can query whatever attributes I like, and print several
>corresponding tables to separate files.
>I haven't used R in years, so I was hoping somebody might be able to
>suggest a solution or combinatin of functions that could help me get
>Right now, I can import my data into a data frame that looks like this:
>df <-
>> df
>    case  gene issue
>1 case_1 gene1  nsyn
>2 case_1 gene1   amp
>3 case_2 gene1   del
>4 case_3 gene2   UTR
>I'd like to cook up some combination of functions/scripting that can
>convert a table like df to produce a list or a data frame/ matrix that
>looks like df2:
>> df2
>        case_1 case_2 case_3
>gene1 nsyn,amp    del      0
>gene2        0      0    UTR
>I can build df2 manually, like this:
>but obviously do not want to do this by hand; I want R to generate df2 from
>Any pointers/ideas would be most welcome!
>    [[alternative HTML version deleted]]
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>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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