Man pages for danielbraas/MetabFUN
This is a collection of functions that I use for metabolomics data analysis

AAA character vector of amino acids.
AbbrevA data frame with metabolite naming conventions used in this...
AdenineA character vector of adenine-related compounds.
barThis function produces a bar plot using data from function...
bar_plotThis function produces a bar plot using data from function...
CoAsA character vector of co-enzyme A-related compounds.
colorsA character vector of commonly used colors.
CompMZA data frame with compound information for 15710 from the...
compound.pathwayA data frame of 3443 KEGG metabolites and their association...
compoundsA data frame of 18042 KEGG compounds.
CurrA character vector of currency metabolites.
CysA character vector of cysteine metabolism compounds.
CytosineA character vector of cytosine-related compounds.
data_annotateThis function is searching either the KEGG or HMDB databases...
FAA character vector of fatty acid-related compounds.
FruA character vector of fructose metabolism compounds.
gene.pathwayA data frame of genes associated with 319 KEGG pathways. This...
glycolysisA character vector of glycolysis compounds.
GuanineA character vector of guanine metabolism compounds.
HexA character vector of hexose metabolism compounds.
isobarThis function takes in an m/z value and will return all...
isomerThis function takes in a chemical formula and will return all...
isomer_KEGGThis function takes in a chemical formula and will return all...
KEGG.pathwayA data frame with 514 KEGG pathways and their corresponding...
make_AOV_volcanoThis function takes in a data and produces a volcano plot...
make_FCThis function produces a data frame with fractional...
make_INCACreate a tab-delimited file with MDVs and a csv file with FC...
make_INCA_normalizedCreates a csv file with flux estimates relative to a control...
make_labeledThis function produces a data frame with percent labeled...
make_line_graphThis function produces a data frame with mass isotopologue...
make_matrixThis function produces a matrix for hierarchical clustering...
make_MIDThis function produces a data frame with mass isotopologue...
make_mzXMLThis function converts .raw files into .mzXML files for...
make_PCAThis function takes in a data matrix and produces a PCA plot...
make_PCA2This function takes in a data matrix and produces a PCA plot...
make_pheatmapThis function takes in a data matrix and produces an...
make_RelAmountsThis function produces a data frame with relative metabolite...
make_unlabeledThis function produces a data frame with fractional...
make_volcanoThis function produces a volcano plot using data with two...
mapvaluesThis function uses the mapvalues function from plyr without...
NeurotransA character vector of neurotransmitter compounds.
normalA character vector of colors used in heatmaps.
pathsA list with all information for 319 KEGG pathways.
PPPA character vector of pentose phosphate metabolism compounds.
purineA character vector of purine metabolism compounds.
pyrimidineA character vector of pyrimidine metabolism compounds.
QEA character vector of compounds to be used as MID inputs for...
TCAA character vector of Tricarboxylic acid (TCA) metabolism...
ThymineA character vector of thymine metabolism compounds.
UracilA character vector of uracil metabolism compounds.
danielbraas/MetabFUN documentation built on Oct. 9, 2020, 9:49 a.m.