R help - Mar 2012 - basic subset question of matrix

Dear list,

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.

Many thanks,
Peter

I think you want:

index <- row.names(myMatrix)  %in% list_to_keep[,1]

This will give a boolean expression as long as the number of rows in
myMatrix; your original only had a list as long as list_to_keep

On Sat, Mar 31, 2012 at 12:26 PM, Peter Davidsen <pkdavidsen at gmail.com>
wrote:
> Dear list,
>
> 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.
>
> Many thanks,
> Peter
>
> ______________________________________________
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-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.