Hi Arun,
That seemed to do the trick - thanks!!
Jonathan
On Wed, Oct 23, 2013 at 11:12 PM, arun <smartpink...@yahoo.com> wrote:
> HI,
>
> Better would be:
> res1 <- dcast(df,gene~case,value.var="issue",paste,collapse=",",fill="0")
>
> str(res1)
> #'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"
>
> write.table(res1,"test.txt",sep="\t",quote=FALSE,row.names=FALSE)
>
>
> A.K.
>
>
> On , arun <smartpink...@yahoo.com> wrote:
> Hi Jonathan,If you look at the str()
> str(res)
> '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})
>
>
> str(res)
> #'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"
>
> write.table(res,"test.txt",sep="\t",quote=FALSE,row.names=FALSE)
>
>
> A.K.
>
>
>
>
>
> On Wednesday, October 23, 2013 10:44 PM, Jon BR <jonsle...@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'
>
>
> Best,
> Jonathan
>
>
>
>
>
>
> On Wed, Oct 23, 2013 at 9:50 PM, arun <smartpink...@yahoo.com> wrote:
>
> HI,
> >
> >You may try:
> >library(reshape2)
> >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
> >
> >
> >A.K.
> >
> >
> >
> >On Wednesday, October 23, 2013 7:38 PM, Jon BR <jonsle...@gmail.com>
> wrote:
> >Hello,
> > 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
> >oriented..
> >
> >Right now, I can import my data into a data frame that looks like this:
> >
> >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"))
> >> 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:
> >df2
>
> ><-data.frame(case_1=c("nsyn,amp","0"),case_2=c("del","0"),case_3=c("0","UTR"))
> >rownames(df2)<-c("gene1","gene2")
> >
> >but obviously do not want to do this by hand; I want R to generate df2
> from
> >df.
> >
> >Any pointers/ideas would be most welcome!
> >
> >Thanks,
> >Jonathan
> >
> > [[alternative HTML version deleted]]
> >
> >
> >______________________________________________
> >R-help@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
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