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| multi_opls <- function(df, group, method){
library(ropls)
colnames(group) <- c('sample','group_name')
group[,2] = as.character(group[,2])
group_num <- as.numeric(length(unique(group[,2])))
group_unique <- as.character(unique(group[,2]))
for (i in 1:(group_num - 1)) {
for (j in (i+1):group_num) {
dir.create(paste(group_unique[i],' VS ',group_unique[j], sep = ''))
selected_group <- c(group_unique[i],group_unique[j])
group_sub <- dplyr::filter(group, group_name %in% selected_group)
df_sub <- df[group_sub$sample,]
if (method == 'opls') {
opls_res <- opls(df_sub,group_sub$group_name)
sample_scores <- as.data.frame(opls_res@scoreMN)
loading_scores <- as.data.frame(opls_res@loadingMN)
modelDF <- as.data.frame(opls_res@modelDF)
vip_value <- as.data.frame(opls_res@vipVn)
}
else {
oplsda_res <- opls(df_sub,
group_sub$group_name,
predI = 1,
orthoI = NA)
sample_scores <- as.data.frame(oplsda_res@scoreMN)
loading_scores <- as.data.frame(oplsda_res@loadingMN)
modelDF <- as.data.frame(oplsda_res@modelDF)
vip_value <- as.data.frame(oplsda_res@vipVn)
}
write.csv(sample_scores,
file = paste(group_unique[i],' VS ',group_unique[j],
'/',
'sample_scores.csv',sep = ''))
write.csv(loading_scores,
file = paste(group_unique[i],' VS ',group_unique[j],
'/',
'loading_scores.csv',sep = ''))
write.csv(modelDF,
file = paste(group_unique[i],' VS ',group_unique[j],
'/',
'modelDF.csv',sep = ''))
write.csv(vip_value,
file = paste(group_unique[i],' VS ',group_unique[j],
'/',
'vip_value.csv',sep = ''))
}
}
}
R
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