[R] basic subset question of matrix
pkdavidsen at gmail.com
Sat Mar 31 18:26:04 CEST 2012
I would like to subset a large expression matrix based on rownames.
That is, I have a list (as a txt-file) with gene names that matches
some of the rows in my matrix.
I've loaded my matrix as well as gene list using the read.table() command.
myMatrix <- read.table("name_of_file.txt", header=T, row.names=1)
list_to_keep <- read.table("name_of_file.txt", header=T)
Thus, both my objects are data frames (however, "list_to_keep" only
have one column).
How do I remove/filter all the rows in my matrix that don't match the
ones in my list_to_keep data frame?
My initial attempt - although unsuccessful:
index <- list_to_keep[,1] %in% row.names(myMatrix)
subset.data <- myMatrix[index, ]
Alternatively, I could imagine that the subset() command would be
ideal, however I cannot write a functional script with this command.
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