ora_bino {mseapca} | R Documentation |
Over-representation analysis with binomial resampling adjustment
Description
Performs ORA while adjusting for undetected metabolites by binomial resampling.
Usage
ora_bino(SIG, DET, M, method = "naive", probs = c(0.025, 0.975), nsim = 1000, lambda = 5)
Arguments
SIG |
Character vector of significant metabolites. |
DET |
Character vector of detected metabolites. |
M |
Named list of metabolite sets. |
method |
|
probs |
Quantiles for the confidence interval (default 95%). |
nsim |
Number of binomial simulations (default 1000). |
lambda |
Shrinkage parameter used when |
Value
A list containing one matrix. Rows = metabolite sets; columns = lower, median, and upper p-values.
Author(s)
Hiroyuki Yamamoto
Examples
# Example: Metabolome data
data(fasting_mseapca)
SIG <- fasting_mseapca$SIG
DET <- fasting_mseapca$DET
M <- fasting_mseapca$pathway
# Perform ORA using detected metabolites only
B <- ora_bino(SIG, DET, M, method="naive", nsim = 10)
B$`Range of p-values for each pathway`
[Package mseapca version 2.2.1 Index]