library(mseapca)
## Loading required package: XML
# --------
# PCA
# --------
filename <- "sample_data.csv"; # load file
pathname <- "C:/R/mseapca/"; # path
fullpath <- paste(pathname,filename,sep="/") # fullpath
X <- read.csv(fullpath) # load csv file
Z <- as.matrix(X[,3:ncol(X)]) # Z :data matrix
M_ID <- as.character(X[,1]) # Metabolite ID
D <- data.frame(M_ID, Z) # Preparing dataframe for PCA
A <- pca_scaled(D) # PCA for autoscaled data
T <- A[["score"]] # PC score
L <- A[["factor.loading"]] # factor loading
P <- A[["p.value"]] # p-value of factor loading
Q <- A[["q.value"]] # q-value of factor loading
class <- c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2)
plot(T[, 1], T[, 2], col = class)
# ---------------- MSEA by ORA ----------------
filepath <- "C:/R/mseapca/pathway.xml"
M <- read_pathway(filepath)
p <- P[, 1:2]
fl <- L[, 1:2]
ALL <- p[, 1]
# SIG <- p[p[, 2] < 0.05 & fl[, 2] > 0, 1] # positive
SIG <- p[p[, 2] < 0.05 & fl[, 2] < 0, 1] # negative
B <- msea_ora(SIG, ALL, M)
print(B[1])
## $`Result of MSEA(ORA)`
## p.value q.value
## Glycolysis 3.234e-01 0.499477
## Pentose phosphate pathway 4.265e-01 0.528052
## TCA cycle 1.467e-01 0.476629
## Glutamic acid and glutamine metabolism 2.635e-01 0.499477
## Alanine, aspartic acid and asparagine metabolism 2.618e-01 0.499477
## Lysine metabolism 6.313e-01 0.683910
## Valine, leucine and isoleucine metabolism 1.808e-01 0.499477
## Glycine, serine and threonine metabolism 3.266e-01 0.499477
## Cysteine metabolism 1.021e-02 0.066346
## Methionine metabolism 6.771e-01 0.704171
## Shikimic acid metabolism 2.635e-01 0.499477
## Histidine metabolism 1.181e-01 0.438479
## Urea cycle 3.234e-01 0.499477
## Proline metabolism 2.635e-01 0.499477
## Polyamine metabolism 3.177e-02 0.165228
## Tryptophan metabolism 4.265e-01 0.528052
## Tyrosine metabolism 3.465e-01 0.500568
## beta-alanine metabolism 9.768e-03 0.066346
## Taurine metabolism 3.234e-01 0.499477
## Creatine metabolism 5.013e-01 0.592420
## Purine metabolism 3.121e-04 0.004057
## Pyrimidine metabolism 7.639e-02 0.331005
## Ribonucleotide metabolism 3.888e-05 0.001011
## Deoxyribonucleotide 1.000e+00 1.000000
## Conjugated bile acid 5.944e-01 0.671898
## Nicotinic acid metaboilsm 3.852e-01 0.527101