Pearson Correlation Issue
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2.8 years ago
LuisNagano ▴ 90

I'd like to run a Pearson correlation for my gene of interest, for example, I would like to search within my normalized RNA-seq data, all genes with Pearson correlation greater than> 0.9 with my gene of interest.

I ran this code dow but it runs all the genes against all the genes, after that I can filter the genes with Pearson correlation >0.9 against my gene, and this overloads the server, I'd like to run my gene (eg TBX5) against all the genes so not overload the system.

Any sugestion?

library(Hmisc)
tabm <- as.matrix(tab[,1:180])
tabm2 <- round(tabm, digits = 2)
tab_cor = rcorr(t(tabm2), type="pearson")
geneXcor_r <- tab_cor$r[rownames(tab_cor$r) == "TBX5",]
posm <- tabm[which(geneXcor_r > 0.9),]

Pearson Correlation Hmisc Overload server • 614 views
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cor(x = all_genes, y = my_gene, method = "spearman")