[R] selecting the COLUMNS in a dataframe function of the numerical values in a ROW

[William Michels]

Perhaps one of the following two methods:

> zgene = 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"))
> zgene
      TTT TTA ATA ATT
gene1   0   0   1   0
gene2   1   1   0   0
gene3   0   1   0   0
gene4   0   0   0   0
>
> zgene[ , zgene[2,1:4] > 0]
      TTT TTA
gene1   0   0
gene2   1   1
gene3   0   1
gene4   0   0
>
> zgene[ , zgene[rownames(zgene) == "gene2",1:4] > 0]
      TTT TTA
gene1   0   0
gene2   1   1
gene3   0   1
gene4   0   0
>

Best Regards,

Bill.

William Michels, Ph.D.



On Thu, Nov 1, 2018 at 9:07 PM, Bogdan Tanasa <tanasa using gmail.com> wrote:
> 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 using 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 using 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]]
>> >
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