keeping only same gene names in two matrices

Question

[zizigolu]

hello,

I have two matrices of gene IDs with the same dimension but whenever I am trying to measure fscore using them telling

networks have not the same node names

> head(A[,1:4])
          AT1G01060 AT1G01170 AT1G01180 AT1G01260
AT1G01060         0         0         0         0
AT1G01170         0         0         0         0
AT1G01180         0         0         0         0
AT1G01260         0         0         0         0
AT1G01380         0         0         0         0
AT1G01490         0         0         0         0

> dim(A)
[1] 3123 3123

> head(B[,1:4])
          AT5G10140 AT5G11260 AT5G62020 AT5G20240
AT5G10140         0         0         0         0
AT5G11260         0         0         1         0
AT5G62020         0         0         0         0
AT5G20240         0         0         0         0
AT3G54340         0         0         0         0
AT3G27010         0         0         0         0

> dim(B)
[1] 3123 3123

how I can have these two matrices with the same gene names? I mean keeping the same genes and removing which is different between two matrices then two matrices become will have the same genes

thank you

Answer 1

[raffael.azevedo]

Greetings Fereshteh.

If I understood your question, a simple workaround is creating a character vector containing the Arabidopsis gene names you want and subsetting the two matrices by your vector, then you should get only what you want.

Ex.:

> genes <- c("AT3G54340", "AT5G10140")
> new_A <- subset(A, by = genes)
> new_B <- subset(B, by = genes)

[zizigolu]

thank you very much, yes you understood my mean well but the question is , genes coming from where in other word which is my reference for subsetting?

[raffael.azevedo]

Hi Fereshteh,

Your reference should be the genes you want to be the same. Another simple workaround is to use the function:

unique()

ex.:

new_A <- unique(A)
new_B <- unique(B)

you can also bind them by column using cbind() and apply unique() to the new data.frame.

I am not quite sure if this is what you are looking for, but send me a message anytime.

Regards,
R.

[zizigolu]

thank you so much