Re: [R] drop rows

From: Peter Wilkinson <pwilkinson_at_videotron.ca>
Date: Thu 01 Jul 2004 - 14:45:48 EST

his ...

hmmmm looks like your working with microarray data as well .... The actual matrix that I am working with is 19000 x 340

Thanks for the help, that was perfect. I am still getting used to the R language way of doing things.I will look into the apply function as you have written it.

Peter

At 12:22 AM 7/1/2004, Erin Hodgess wrote:
>Hi Peter!
>
>Here is an example:
>
> > x
> [,1] [,2] [,3] [,4] [,5]
> [1,] 2.1632497 0.43219960 0.05329827 0.1484550 2.12996660
> [2,] 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000
> [3,] -1.2230673 0.83467155 -0.14820752 -0.1012919 -0.04410457
> [4,] -0.5397403 0.92664487 -0.30390539 0.3105849 -0.69958321
> [5,] 1.0112805 1.13063148 -1.59802451 0.7597861 -0.72821421
> [6,] -1.1170756 -0.05128944 0.02755781 -0.8896866 0.12294861
> [7,] 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000
> [8,] 0.7043937 0.82557039 -1.38759266 0.5266536 0.67345991
> [9,] 0.7522765 0.25513348 -1.00076227 0.1141770 1.70003769
>[10,] 0.3371948 -1.48590028 -0.67115529 -0.8242699 1.32741665
> > #This takes out the rows with ANY zeros
> > x[!apply(x,1,function(x)any(x)==0),]
> [,1] [,2] [,3] [,4] [,5]
>[1,] 2.1632497 0.43219960 0.05329827 0.1484550 2.12996660
>[2,] -1.2230673 0.83467155 -0.14820752 -0.1012919 -0.04410457
>[3,] -0.5397403 0.92664487 -0.30390539 0.3105849 -0.69958321
>[4,] 1.0112805 1.13063148 -1.59802451 0.7597861 -0.72821421
>[5,] -1.1170756 -0.05128944 0.02755781 -0.8896866 0.12294861
>[6,] 0.7043937 0.82557039 -1.38759266 0.5266536 0.67345991
>[7,] 0.7522765 0.25513348 -1.00076227 0.1141770 1.70003769
>[8,] 0.3371948 -1.48590028 -0.67115529 -0.8242699 1.32741665
> > #This takes out the rows with ALL zeros
> > x[!apply(x,1,function(x)all(x)==0),]
> [,1] [,2] [,3] [,4] [,5]
>[1,] 2.1632497 0.43219960 0.05329827 0.1484550 2.12996660
>[2,] -1.2230673 0.83467155 -0.14820752 -0.1012919 -0.04410457
>[3,] -0.5397403 0.92664487 -0.30390539 0.3105849 -0.69958321
>[4,] 1.0112805 1.13063148 -1.59802451 0.7597861 -0.72821421
>[5,] -1.1170756 -0.05128944 0.02755781 -0.8896866 0.12294861
>[6,] 0.7043937 0.82557039 -1.38759266 0.5266536 0.67345991
>[7,] 0.7522765 0.25513348 -1.00076227 0.1141770 1.70003769
>[8,] 0.3371948 -1.48590028 -0.67115529 -0.8242699 1.32741665
> >
>
> Hope this helps!
> Sincerely,
>Erin Hodgess
>Associate Professor
>Department of Computer and Mathematical Sciences
>University of Houston - Downtown
>mailto: hodgess@gator.uhd.edu
>
>
>
>From: Peter Wilkinson <pwilkinson@videotron.ca>
>Subject: [R] how to drop rows from a data.frame
>
>here is a snippet of data where I would like to drop all rows that have
>zeros across them, and keep the rest of the rows while maintaining the row
>names (1,2,3, ...10). The idea here is that a row of zeros is an indication
>that the row must be dropped. There will never be the case where there is a
>row(of n columns) with less than 5 zeros in this case(n zeros
>
>I am unsure how to manipulate the data frame to drop rows whiles keeping
>row names.
>
>Peter
>
>the data (imagine separated by tabs):
>
> SEKH0001 SEKH0002 SEKH0003 SEKH0004 SEKH0005
> [1,] 256.1139 256.1139 256.1139 256.1139 256.1139
> [2,] 283.0741 695.1000 614.5117 453.0342 500.1436
> [3,] 257.3578 305.0818 257.3578 257.3578 257.3578
> [4,] 0.0000 0.0000 0.0000 0.0000 0.0000
> [5,] 0.0000 0.0000 0.0000 0.0000 0.0000
> [6,] 0.0000 0.0000 0.0000 0.0000 0.0000
> [7,] 0.0000 0.0000 0.0000 0.0000 0.0000
> [8,] 257.0000 257.0000 257.0000 257.0000 257.0000
> [9,] 305.7857 2450.0417 335.5428 305.7857 584.2485
>[10,] 0.0000 0.0000 0.0000 0.0000 0.0000
>
>what I want it to look like:
>
> SEKH0001 SEKH0002 SEKH0003 SEKH0004 SEKH0005
> [1,] 256.1139 256.1139 256.1139 256.1139 256.1139
> [2,] 283.0741 695.1000 614.5117 453.0342 500.1436
> [3,] 257.3578 305.0818 257.3578 257.3578 257.3578
> [8,] 257.0000 257.0000 257.0000 257.0000 257.0000
> [9,] 305.7857 2450.0417 335.5428 305.7857 584.2485
>
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R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Jul 01 14:49:30 2004

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