How to run t-test with subset of rows in R

Question

Below is a part of my data (pairht_protein)

I am trying to run t-test on all the variables (columns) between two groups which are:

Resistant_group <- c(PAIR-01, PAIR-12, PAIR-09)
Sensitive_group <- c(PAIR-07, PAIR-02, PAIR-05)

Before I make a function I tired to pick one of the variables and tried:

t.test(m_pHSL660 ~ Subject, data = subset(pairht_protein, Subject %in% c("Resistant_group", "Sensitive_group")))

But it gave me an error : 'grouping factor must have exactly 2 levels'

Is there a way to run t-test between these groups? and possibly make it as a function?

Answer 1

First, you must correct how you define the groups (you cannot use dashes on variable names):

Resistant_group <- c('PAIR-01', 'PAIR-12', 'PAIR-09')
Sensitive_group <- c('PAIR-07','PAIR-02','PAIR-05')

Then, using dplyr package create another factor variable with only two levels:

library(dplyr)

# assuming pairht_protein is your dataset name

pairht_protein <- pairht_protein %>% mutate(sub = case_when( subject %in% Resistant_group ~1,
                                  subject %in% Sensitive_group ~2),
                          sub = as.factor(sub))

Because this new variable is going to make NAs values for elements outside your groups, you don't need to subsetting:

t.test(m_pHSL660 ~ sub, data =pairht_protein)