R help - Nov 2018 - selecting the COLUMNS in a dataframe function of the numerical values in a ROW

Dear all, please may I ask for a suggestion :

considering a dataframe  that contains the numerical values for gene
expression, for example :

 x = data.frame(TTT=c(0,1,0,0),
               TTA=c(0,1,1,0),
               ATA=c(1,0,0,0),
               gene=c("gene1", "gene2", "gene3",
"gene4"))

how could I select only the COLUMNS where the value of a GENE (a ROW) is
non-zero ?

thank you !

-- bogdan

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This would be a bit simpler if 'gene' were the rownames of the
data.frame.
The '-4' is to remove the gene column from the calculations.
> x[ x[,"gene"]=="gene2",]
  TTT TTA ATA  gene
2   1   1   0 gene2
> colnames(x)[-4][ 1 == x[ x[,"gene"]=="gene2",-4] ]
[1] "TTT" "TTA"
> colnames(x)[-4][ 1 == x[ x[,"gene"]=="gene3",-4] ]
[1] "TTA"
> x
  TTT TTA ATA  gene
1   0   0   1 gene1
2   1   1   0 gene2
3   0   1   0 gene3
4   0   0   0 gene4



Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Nov 1, 2018 at 5:45 PM, Bogdan Tanasa <tanasa at gmail.com> wrote:
> Dear all, please may I ask for a suggestion :
>
> considering a dataframe  that contains the numerical values for gene
> expression, for example :
>
>  x = data.frame(TTT=c(0,1,0,0),
>                TTA=c(0,1,1,0),
>                ATA=c(1,0,0,0),
>                gene=c("gene1", "gene2",
"gene3", "gene4"))
>
> how could I select only the COLUMNS where the value of a GENE (a ROW) is
> non-zero ?
>
> thank you !
>
> -- bogdan
>
>         [[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 Bogdan,

Are you saying you want to drop columns that sum to zero? If so, I'm
not sure you've given us a good example dataframe, since all your
numeric columns give non-zero sums.

Otherwise, what you're asking for is trivial. Below is an example
dataframe ("ygene") with an example "AGA" column that gets
dropped:
> xgene <- data.frame(TTT=c(0,1,0,0),
+                TTA=c(0,1,1,0),
+                ATA=c(1,0,0,0),
+                gene=c("gene1", "gene2", "gene3",
"gene4"))
>
> xgene[ , colSums(xgene[,1:3]) > 0 ]
  TTT TTA ATA  gene
1   0   0   1 gene1
2   1   1   0 gene2
3   0   1   0 gene3
4   0   0   0 gene4
>
> ygene <- data.frame(TTT=c(0,1,0,0),
+                 TTA=c(0,1,1,0),
+                 AGA=c(0,0,0,0),
+                 gene=c("gene1", "gene2",
"gene3", "gene4"))
>
> ygene[ , colSums(ygene[,1:3]) > 0 ]
  TTT TTA  gene
1   0   0 gene1
2   1   1 gene2
3   0   1 gene3
4   0   0 gene4


HTH,

Bill.

William Michels, Ph.D.


On Thu, Nov 1, 2018 at 5:45 PM, Bogdan Tanasa <tanasa at gmail.com>
wrote:
> Dear all, please may I ask for a suggestion :
>
> considering a dataframe  that contains the numerical values for gene
> expression, for example :
>
>  x = data.frame(TTT=c(0,1,0,0),
>                TTA=c(0,1,1,0),
>                ATA=c(1,0,0,0),
>                gene=c("gene1", "gene2",
"gene3", "gene4"))
>
> how could I select only the COLUMNS where the value of a GENE (a ROW) is
> non-zero ?
>
> thank you !
>
> -- bogdan
>
>         [[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.

Dear Bill, and Bill,

many thanks for taking the time to advice, and for your suggestions. I
believe that I shall rephrase a bit my question, with a better example :
thank you again in advance for your help.

Let's assume that we start from a data frame :

x = data.frame(  TTT=c(0,1,0,0),
               TTA=c(0,1,1,0),
                ATA=c(1,0,0,0),
                 ATT=c(0,0,0,0),
                row.names=c("gene1", "gene2",
"gene3", "gene4"))

Shall we select "gene2", at the end, we would like to have ONLY the
COLUMNS, where "gene2" is NOT-ZERO. In other words, the output
contains
only the first 2 columns :

output = data.frame(  TTT=c(0,1,0,0),
                                   TTA=c(0,1,1,0),
                                   row.names=c("gene1",
"gene2", "gene3",
"gene4"))

 with much appreciation,

-- bogdan

On Thu, Nov 1, 2018 at 6:34 PM William Michels <wjm1 at caa.columbia.edu>
wrote:
> Hi Bogdan,
>
> Are you saying you want to drop columns that sum to zero? If so, I'm
> not sure you've given us a good example dataframe, since all your
> numeric columns give non-zero sums.
>
> Otherwise, what you're asking for is trivial. Below is an example
> dataframe ("ygene") with an example "AGA" column that
gets dropped:
>
> > xgene <- data.frame(TTT=c(0,1,0,0),
> +                TTA=c(0,1,1,0),
> +                ATA=c(1,0,0,0),
> +                gene=c("gene1", "gene2",
"gene3", "gene4"))
> >
> > xgene[ , colSums(xgene[,1:3]) > 0 ]
>   TTT TTA ATA  gene
> 1   0   0   1 gene1
> 2   1   1   0 gene2
> 3   0   1   0 gene3
> 4   0   0   0 gene4
> >
> > ygene <- data.frame(TTT=c(0,1,0,0),
> +                 TTA=c(0,1,1,0),
> +                 AGA=c(0,0,0,0),
> +                 gene=c("gene1", "gene2",
"gene3", "gene4"))
> >
> > ygene[ , colSums(ygene[,1:3]) > 0 ]
>   TTT TTA  gene
> 1   0   0 gene1
> 2   1   1 gene2
> 3   0   1 gene3
> 4   0   0 gene4
>
>
> HTH,
>
> Bill.
>
> William Michels, Ph.D.
>
>
> On Thu, Nov 1, 2018 at 5:45 PM, Bogdan Tanasa <tanasa at gmail.com>
wrote:
> > Dear all, please may I ask for a suggestion :
> >
> > considering a dataframe  that contains the numerical values for gene
> > expression, for example :
> >
> >  x = data.frame(TTT=c(0,1,0,0),
> >                TTA=c(0,1,1,0),
> >                ATA=c(1,0,0,0),
> >                gene=c("gene1", "gene2",
"gene3", "gene4"))
> >
> > how could I select only the COLUMNS where the value of a GENE (a ROW)
is
> > non-zero ?
> >
> > thank you !
> >
> > -- bogdan
> >
> >         [[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]]