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: [EMAIL PROTECTED]
From: Peter Wilkinson <[EMAIL PROTECTED]> 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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