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library(httr) | |
library(rmzTabM) | |
library(xcms) | |
library(faahKO) | |
data(faahko3) | |
faahkoMzTab <- rmzTabM::MzTab$new( | |
metadata=Metadata$new( | |
'mzTab-version' = "2.2.0-M", | |
'mzTab-ID' = "faahKO", |
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- id: chemont | |
preferredPrefix: ChemOnt | |
title: ChemOnt: A semantic-based ontology for chemical and biological data integration. | |
uri: http://classyfire.wishartlab.com/ | |
description: "ChemOnt is comphrehensive, computable, and manually curated. | |
It covers >4000 chemical classes of organic and inorganic compounds. The set of classes was created | |
and extended by extracting common terms from the scientific literature (e.g.: IUPAC) and available databases. | |
The flexibility The taxonomy is currently mapped to the ChEBI and LIPID MAPS ontologies in collaboration | |
with the respective teams. Moreover, ChemOnt has been partially mappped to the MeSH thesaurus. | |
The mapping effort in this regard is ongoing. Thanks to the flexibility and simplicity of its structure |
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## TODO: | |
## study-variable , separated -> DONE | |
## assay[1]-assay[2]-assay[3]-assay[4]-assay[5]-assay[6] | |
## link sample - assay: | |
## | |
## MTD sample[1]-description KO15 | |
## MTD assay[1]-sample_ref sample[1] | |
library(plyr) ## for rbind.fill |
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library(multtest) | |
## A convenience function cut&paste from | |
## https://github.com/sneumann/xcms/blob/master/R/xcmsSet.R#L2052 | |
pval <- function(X, classlabel, teststat) { | |
n1 <- rowSums(!is.na(X[,classlabel == 0])) | |
n2 <- rowSums(!is.na(X[,classlabel == 1])) | |
A <- apply(X[,classlabel == 0], 1, sd, na.rm=TRUE)^2/n1 ## sd(t(X[,classlabel == 0]), na.rm = TRUE)^2/n1 |
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