R/data.R

In graeberlab-ucla/MetabR: MetabR: UCLA Metabolomics QC Analysis Pipeline

#' A character vector of amino acids.
#'
#'@format A character vector of length 22.
"AA"

#' A data frame with metabolite naming conventions used in this package.
#'
#'@format A data frame with seven variables and 204 entries
"Abbrev"

#' A character vector of adenine-related compounds.
#'
#'@format A character vector of length 13.
"Adenine"

#' A character vector of co-enzyme A-related compounds.
#'
#'@format A character vector of length 9.
"CoAs"

#' A data frame with compound information for 15710 from the KEGG database as well as 41500 HMDB
#' compounds. The compounds are overlapping and also include calculated mass-to-charge values for 111
#' salt clusters.
#'
#'@format A data frame of 6294970 rows and 12 variables.
"CompMZ"

#' A character vector of currency metabolites.
#'
#'@format A character vector of length 16.
"Curr"

#' A character vector of cysteine metabolism compounds.
#'
#'@format A character vector of length 11.
"Cys"

#' A character vector of cytosine-related compounds.
#'
#'@format A character vector of length 9.
"Cytosine"

#' A character vector of fatty acid-related compounds.
#'
#'@format A character vector of length 11.
"FA"

#' A character vector of fructose metabolism compounds.
#'
#'@format A character vector of length 9.
"Fru"

#' A character vector of guanine metabolism compounds.
#'
#'@format A character vector of length 8.
"Guanine"

#' A character vector of hexose metabolism compounds.
#'
#'@format A character vector of length 8.
"Hex"

#' A data frame with 514 KEGG pathways and their corresponding IDs.
#'
#'@format A data frame with 514 rows and 2 variables.
"KEGG.pathway"

#' A character vector of neurotransmitter compounds.
#'
#'@format A character vector of length 5.
"Neurotrans"

#' A character vector of pentose phosphate metabolism compounds.
#'
#'@format A character vector of length 14.
"PPP"

#' A character vector of compounds to be used as MID inputs for INCA.
#'
#'@format A character vector of length 12.
"QE"

#' A character vector of Tricarboxylic acid (TCA) metabolism compounds.
#'
#'@format A character vector of length 14.
"TCA"

#' A character vector of uracil metabolism compounds.
#'
#'@format A character vector of length 7.
"Uracil"

#' A data frame of 3443 KEGG metabolites and their association with 319 KEGG pathways.
#'
#'@format A data frame of 5860 rows and 5 variables.
"compound.pathway"

#' A data frame of 18042 KEGG compounds.
#'
#'@format A data frame of 18042 rows and 4 variables.
"compounds"

#' A data frame of genes associated with 319 KEGG pathways. This data frame is useful for
#' gene set enrichment analysis if reshaped.
#'
#'@format A data frame of 25580 rows and 8 variables.
"gene.pathway"

#' A character vector of glycolysis compounds.
#'
#'@format A character vector of length 26.
"glycolysis"

#' A character vector of colors used in heatmaps.
#'
#'@format A character vector of length 3.
"normal"

#' A list with all information for 319 KEGG pathways.
#'
#'@format A character vector of length 7.
"paths"

#' A character vector of purine metabolism compounds.
#'
#'@format A character vector of length 7.
"purine"

#' A character vector of pyrimidine metabolism compounds.
#'
#'@format A character vector of length 7.
"pyrimidine"

#' A character vector of thymine metabolism compounds.
#'
#'@format A character vector of length 5.
"Thymine"