Correlation mutual rank calculation

Question

[pr2009]

Hi

I have a correlation matrix for 34704 genes (size: 24GB). Is it possible to calculate the mutual rank of this file in R studio?

# correlation rank matrix
R <- t(apply(1-C, 1, rank))

# mutual rank matrix
M <- sqrt(R * t(R))

[Ram]

R studio is a development environment/tool, R is the language. You're looking for a solution in R, not R studio.

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[pr2009]

Thank you for your suggestions.

I am aware of the difference between R and R studio. My question was whether I can use a big file of 24GB in R studio (Desktop)

Apologies for not being clear.

Best Regards

[Jean-Karim Heriche]

You can do it in RStudio as long as your computer does have enough RAM. The main issue will probably be the time it takes to read the file.

Answer 1

[Jean-Karim Heriche]

The correlation ranks have to be calculated relative to each gene separately. Try something like this:

R <- matrix(NA, nrow = number.of.genes, ncol = number.of.genes)   
# Compute correlation ranks for each gene
for(i in 1:number.of.genes) {
    # Rank all genes relative to gene i
    # Use 1-cor() because rank() uses ascending order
    R[i,] <- rank(apply(gene.data, 1, function(x) 1-cor(t(gene.data[i,]),x)))
}
M <- sqrt(R *t(R)) # Mutual rank

[pr2009]

Thank you for getting back. Much appreciated.