subset matrix based on cell values

Question

This should be simple, but I cannot figure it out:

I have a square matrix with integer values in each cell (result of an all vs all distance calculation). I would like to subset the matrix based on the cell values, e.g. cell == 8, or cell <= 6 , etc.

foo[1:5, 1:5]
                CASSLLAGAPEQFF CASSQVGLATGTQYF CASSSGTQYTQYF CASRITSGGKTQYF CATSDSRGKTQYF
CASSLLAGAPEQFF               0             999           999              8           999
CASSQVGLATGTQYF            999               0           999            999           999
CASSSGTQYTQYF              999             999             0            999             6
CASRITSGGKTQYF               8             999           999              0           999
CATSDSRGKTQYF              999             999             6            999             0

dput:

structure(c(0, 999, 999, 8, 999, 999, 0, 999, 999, 999, 999, 999, 0, 999, 6, 8, 999, 999, 0, 999, 999, 999, 6, 999, 0), .Dim = c(5L, 5L), .Dimnames = list(c("CASSLLAGAPEQFF", "CASSQVGLATGTQYF", "CASSSGTQYTQYF", "CASRITSGGKTQYF", "CATSDSRGKTQYF"), c("CASSLLAGAPEQFF", "CASSQVGLATGTQYF", "CASSSGTQYTQYF", "CASRITSGGKTQYF", "CATSDSRGKTQYF" )))

Expected result of cell == 8 would be a 2x2 matrix of

               CASSLLAGAPEQFF  CASRITSGGKTQYF
CASSLLAGAPEQFF 0                8
CASRITSGGKTQYF 8                0

The row and column names don't matter to the subsetting (but I want to keep the names). What is the most straightforward way to do that?

Thanks for your help!

Please use dput to show a small example of what you have. When you say "all vs all distance calculation" do you mean you've used dist and now have an object of class dist? — Roland
Please add dput(foo[1:5, 1:5]) to the question and also show the expected result. — Roland

cryo111 cryo111 · Accepted Answer · 2015-11-20T18:57:01

You can replace the ==8 with any other filtering criterion.

foo[rowSums(foo==8)>0,colSums(foo==8)>0]
#               CASSLLAGAPEQFF CASRITSGGKTQYF
#CASSLLAGAPEQFF              0              8
#CASRITSGGKTQYF              8              0

rowSums(foo==8)>0 finds any row where at least one element of foo==8 is TRUE. colSums(foo==8)>0 does the same for each column.

subset matrix based on cell values

1 Answers