How to perform enrichment p-value for a motif

Question

[Apex92]

I have a data frame that looks like below.

Category,Total_Genes,UUAGGG_motif
Background,22591,18190
SetA,122,102
SetB,198,182
SetC,90,82

I have counted the number of motifs available in each category. Now I want to calculate three p-value (SetA vs Background - SetB vs background and SetC vs background) to see in which of the three categories the motif is enriched considering the size of each category.

I came up with this approach in R - is this the correct way? Thank you in advance.

library(hypeR)

# Number of background genes
N <- 22591
# Number of background genes with motif
K <- 18190

# Set A
n_A <- 122
k_A <- 102

# Set B
n_B <- 198
k_B <- 182

# Set C
n_C <- 90
k_C <- 82

# Perform hypergeometric test for Set A
p_value_A <- 1 - phyper(k_A - 1, K, N - K, n_A, lower.tail = TRUE)

# Perform hypergeometric test for Set B
p_value_B <- 1 - phyper(k_B - 1, K, N - K, n_B, lower.tail = TRUE)

# Perform hypergeometric test for Set C
p_value_C <- 1 - phyper(k_C - 1, K, N - K, n_C, lower.tail = TRUE)

[Trivas]

This seems like a good time to use MEME suite of tools. You can use something like IUPAC2MEME to get your PWM then a tool like centrimo with your gene list and your background list.