I have a sheet containing numeric pathway scores and non-numeric Mutation status (e.g., MUT and WT) of the gene. I wish to compute the Spearman correlation coefficient and p-values of each pathway (numeric data) with each of the gene mutation status. Which package in R should I prefer to choose? I tried using cor package in R, but it gives error as it imports only numeric data type.
I have a data like this and i used cor function to compute Sperman Rank correlation coeffient. It's giving values but i'm not able to understand these values are with respect to what (MUT or WT) as its giving a single value of each gene column with respect to each pathway.
AGTR2(Gene) Alanine.and.aspartate.metabolism MUT 0 MUT 0.041389321 WT 0.016554228 WT 0.172155284
I used this script for my analysis
Col_data <- read.table(file = "Data.txt", header = T, sep = "\t") A <- cor(rank(Col_data$AGTR2), rank(Col_data$Alanine.and.aspartate.metabolism)) B <- cor(rank(Col_data$AGTR2), rank(Col_data$Amino.and.nucleotide.sugar.metabolism))
and so on...