Subsetting a matrix by row.names

Question

I have a matrix with the following row.names:

"X1"   "X5"   "X33"  "X37"  "X52"  "X566"

Now I want to select only the rows which match the entries of a list, say:

include_list <- c("X1", "X5", "X33")

I imagine I'd do something like this:

data.subset <- subset(data, row.names == include_list)

However, this particular code does not seem to do the job. How can I perform subsetting in this way?

Answer 1

Set up some fake data:

m <- matrix(1:30, 6, 5)
rownames(m) <- c("X1", "X5", "X33", "X37", "X52", "X566")
m
#      [,1] [,2] [,3] [,4] [,5]
# X1      1    7   13   19   25
# X5      2    8   14   20   26
# X33     3    9   15   21   27
# X37     4   10   16   22   28
# X52     5   11   17   23   29
# X566    6   12   18   24   30

Here it's probably easiest to subset with matrix indexing ([):

include_list <- c("X1", "X5", "X33")
m[include_list, ]
#     [,1] [,2] [,3] [,4] [,5]
# X1     1    7   13   19   25
# X5     2    8   14   20   26
# X33    3    9   15   21   27

Alternative with subset() function:

subset(m, rownames(m) %in% include_list)
#      [,1] [,2] [,3] [,4] [,5]
# X1     1    7   13   19   25
# X5     2    8   14   20   26
# X33    3    9   15   21   27

Answer 2

This also seems to work:

include_list <- head(read.csv("/Users/histelheim/include_list.csv", header = FALSE))
include_list <- c(do.call("cbind", include_list)) 
data[row.names(data) %in% include_list, ]