Pearson Correlation Issue
0
0
Entering edit mode
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
ADD COMMENT
1
Entering edit mode

cor(x = all_genes, y = my_gene, method = "spearman")

ADD REPLY

Login before adding your answer.

Traffic: 1989 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6