R help - Jan 2016 - [Q] It it possible to create the data frame only non-zero data column?

Hello all.

I re-post this question by e-mail.
(I posted via google-group. But It's not posted yet.)

I'm newbie GNU R.

I would like to compare two datas.
How to select columns which has non-zero datas?.
It it possible to create the data frame only VAL3(non-zero data) column
with command?

Formatted sample.
https://gist.github.com/hiroyuki-sato/cb36584f6cd5845b6c3e

sample1.txt

  ID,VAL1,VAL2,VAL3
  ID1,0,2,3
  ID2,0,2,3
  ID3,0,2,3

  real data has 5000 columns.

sample2.txt

  ID,VAL1,VAL2,VAL3
  ID1,0,2,3
  ID2,0,2,3
  ID3,0,2,2

  The difference sample1 and sample2 is ID3/VAL3.
    sample1: 3
    sample2: 2

R commands.

  sample1 <- read.table("sample1.txt",header=T,sep=',')
  sample2 <- read.table("sample2.txt",header=T,sep=',')

  result <- sample1[,2:4] - sample2[,2:4]
  result
    VAL1 VAL2 VAL3
  1    0    0    0
  2    0    0    0
  3    0    0    1

I would like to create data frame which has non-zero value columns.
Could you tell me how to do it?

Best regards.

--
Hiroyuki Sato.

	[[alternative HTML version deleted]]

Could you use rowsum and select rows larger then 0?

Something like:

result[rowsum(as.matrix(result) > 0, ]

On Fri, 8 Jan 2016 at 18:00 Hiroyuki Sato <hiroysato at gmail.com> wrote:
> Hello all.
>
> I re-post this question by e-mail.
> (I posted via google-group. But It's not posted yet.)
>
> I'm newbie GNU R.
>
> I would like to compare two datas.
> How to select columns which has non-zero datas?.
> It it possible to create the data frame only VAL3(non-zero data) column
> with command?
>
> Formatted sample.
> https://gist.github.com/hiroyuki-sato/cb36584f6cd5845b6c3e
>
> sample1.txt
>
>   ID,VAL1,VAL2,VAL3
>   ID1,0,2,3
>   ID2,0,2,3
>   ID3,0,2,3
>
>   real data has 5000 columns.
>
> sample2.txt
>
>   ID,VAL1,VAL2,VAL3
>   ID1,0,2,3
>   ID2,0,2,3
>   ID3,0,2,2
>
>   The difference sample1 and sample2 is ID3/VAL3.
>     sample1: 3
>     sample2: 2
>
> R commands.
>
>   sample1 <-
read.table("sample1.txt",header=T,sep=',')
>   sample2 <-
read.table("sample2.txt",header=T,sep=',')
>
>   result <- sample1[,2:4] - sample2[,2:4]
>   result
>     VAL1 VAL2 VAL3
>   1    0    0    0
>   2    0    0    0
>   3    0    0    1
>
> I would like to create data frame which has non-zero value columns.
> Could you tell me how to do it?
>
> Best regards.
>
> --
> Hiroyuki Sato.
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
	[[alternative HTML version deleted]]

Hi

as.matrix is rather dangerous, it converts all values to lowest mode which, if
there is text column, is character.

And if I understand correctly original post was about removing all zero columns.

Using plain zero comparison can be dangerous due to possibility of compensating
negative and positive values.
> dat<-data.frame(a=c(-1,0,1), b=c(0,0,0), c=c(0,0,1))
> dat
   a b c
1 -1 0 0
2  0 0 0
3  1 0 1
> colSums(dat)==0
    a     b     c
 TRUE  TRUE FALSE

Remove incorrectly first column too.

I would proceed with NA substitution, which is safer.
> dat[dat==0]<-NA
> colSums(is.na(dat))==nrow(dat)
    a     b     c
FALSE  TRUE FALSE
>
And even this can be problematic if values in dat are not integers.

Cheers
Petr
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Ulrik
> Stervbo
> Sent: Friday, January 08, 2016 6:06 PM
> To: Hiroyuki Sato; r-help at r-project.org
> Subject: Re: [R] [Q] It it possible to create the data frame only non-
> zero data column?
>
> Could you use rowsum and select rows larger then 0?
>
> Something like:
>
> result[rowsum(as.matrix(result) > 0, ]
>
> On Fri, 8 Jan 2016 at 18:00 Hiroyuki Sato <hiroysato at gmail.com>
wrote:
>
> > Hello all.
> >
> > I re-post this question by e-mail.
> > (I posted via google-group. But It's not posted yet.)
> >
> > I'm newbie GNU R.
> >
> > I would like to compare two datas.
> > How to select columns which has non-zero datas?.
> > It it possible to create the data frame only VAL3(non-zero data)
> > column with command?
> >
> > Formatted sample.
> > https://gist.github.com/hiroyuki-sato/cb36584f6cd5845b6c3e
> >
> > sample1.txt
> >
> >   ID,VAL1,VAL2,VAL3
> >   ID1,0,2,3
> >   ID2,0,2,3
> >   ID3,0,2,3
> >
> >   real data has 5000 columns.
> >
> > sample2.txt
> >
> >   ID,VAL1,VAL2,VAL3
> >   ID1,0,2,3
> >   ID2,0,2,3
> >   ID3,0,2,2
> >
> >   The difference sample1 and sample2 is ID3/VAL3.
> >     sample1: 3
> >     sample2: 2
> >
> > R commands.
> >
> >   sample1 <-
read.table("sample1.txt",header=T,sep=',')
> >   sample2 <-
read.table("sample2.txt",header=T,sep=',')
> >
> >   result <- sample1[,2:4] - sample2[,2:4]
> >   result
> >     VAL1 VAL2 VAL3
> >   1    0    0    0
> >   2    0    0    0
> >   3    0    0    1
> >
> > I would like to create data frame which has non-zero value columns.
> > Could you tell me how to do it?
> >
> > Best regards.
> >
> > --
> > Hiroyuki Sato.
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
> >
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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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