R help - Jun 2011 - counting columns that fulfill specific criteria

Hi,

I have a matrix (pwdiff in the example below) with ~480000 rows and 780
columns.
For each row, I want to get the percentage of columns that have an absolute
value above a certain threshold "t". I then want to allocate that
percentage
to matrix 'perc' in the corresponding row. Below is my attempt at doing
this, but it does not work: I get 'replacement has length zero'. Any
help
would be much appreciated!!

perc<-matrix(c(1:nrow(pwdiff)))
for (x in 1:nrow(pwdiff))
perc[x]<-(((ncol(pwdiff[,abs(pwdiff[x,]>=t)]))/ncol(pwdiff))*100)

I should add that my data has NAs in some rows and not others (but I do not
want to just ignore rows that have NAs)

Thanks!

Paul

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Hi

> Hi,
> 
> I have a matrix (pwdiff in the example below) with ~480000 rows and 780
> columns.
> For each row, I want to get the percentage of columns that have an 
absolute
> value above a certain threshold "t". I then want to allocate that
percentage
> to matrix 'perc' in the corresponding row. Below is my attempt at
doing
> this, but it does not work: I get 'replacement has length zero'.
Any
help
> would be much appreciated!!
> 
> perc<-matrix(c(1:nrow(pwdiff)))
> for (x in 1:nrow(pwdiff))
> perc[x]<-(((ncol(pwdiff[,abs(pwdiff[x,]>=t)]))/ncol(pwdiff))*100)
As 
> matrix(c(1:nrow(pwdiff)))
Error in nrow(pwdiff) : object 'pwdiff' not
found
>
gives an error we cannot directly check your code.
>From what you say it seems to me that you want something like
 rowSums(pwdiff>=t, na.rm=T)/ncol(pwdiff)*100

or maybe

rowSums(abs(pwdiff)>=t, na.rm=T)/ncol(pwdiff)*100

but I can be completely wrong.

Regards
Petr
> 
> I should add that my data has NAs in some rows and not others (but I do 
not
> want to just ignore rows that have NAs)
> 
> Thanks!
> 
> Paul
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/counting-
> columns-that-fulfill-specific-criteria-tp3622265p3622265.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at 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.

Hello Paul.

You could try something like
perc<-apply(pwdiff, 1 function(currow){
	mean(abs(currow) > t, na.rm=TRUE)*100
})

I haven't tested this, as you did not provide a sample pwdiff. You should
probably check ?apply for more info.

Two suggestions: probably best not to name any variable t, as this is also
the function for transposing a matrix, and could end up being confusing at
the least. Second: for most practical purposes, it's better to leave out the
*100.

Good luck,


Nick Sabbe
--
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link: http://biomath.ugent.be
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ring: 09/264.59.36

-- Do Not Disapprove



> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of pguilha
> Sent: vrijdag 24 juni 2011 13:15
> To: r-help at r-project.org
> Subject: [R] counting columns that fulfill specific criteria
> 
> Hi,
> 
> I have a matrix (pwdiff in the example below) with ~480000 rows and 780
> columns.
> For each row, I want to get the percentage of columns that have an
> absolute
> value above a certain threshold "t". I then want to allocate that
> percentage
> to matrix 'perc' in the corresponding row. Below is my attempt at
doing
> this, but it does not work: I get 'replacement has length zero'.
Any
> help
> would be much appreciated!!
> 
> perc<-matrix(c(1:nrow(pwdiff)))
> for (x in 1:nrow(pwdiff))
> perc[x]<-(((ncol(pwdiff[,abs(pwdiff[x,]>=t)]))/ncol(pwdiff))*100)
> 
> I should add that my data has NAs in some rows and not others (but I do
> not
> want to just ignore rows that have NAs)
> 
> Thanks!
> 
> Paul
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/counting-
> columns-that-fulfill-specific-criteria-tp3622265p3622265.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at 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.