#' Returns default list for identifier and data types to import
#'
#' @param data.type datatype
#'
#' @return
#' @export
#'
#'
get_MaxQuant_defaults <- function(data.type) {
defaults <- list(
# proteinGroups
proteinGroups = list(identifier = c("Protein.IDs"),
data.columns = c("Gene.names",
"Protein.names",
"Peptides",
"LFQ.intensity",
"id",
"Only.identified.by.site",
"Potential.contaminant",
"Reverse")),
# peptides
peptides = list(identifier = c("Leading.razor.protein",
"Start.position",
"End.position"),
data.columns = c("LFQ.intensity",
"Experiment",
"Protein.group.IDs",
"id",
"Potential.contaminant",
"Reverse")),
# modificationSpecificPeptides
modificationSpecificPeptides = list(identifier = c("Proteins",
"id"),
data.columns = c("Proteins",
"Protein.group.IDs",
"Peptide.ID",
"Experiment",
"id",
"Potential.contaminant",
"Reverse")),
# Sites
Sites = list(identifier = c(c("Proteins",
"Amino.acid",
"Positions.within.proteins")),
data.columns = c("Proteins",
"Localization.prob",
"Amino.acid",
"Positions.within.proteins",
"id",
"Potential.contaminant",
"Reverse"))
# proteinGroups = list(identifier = c(),
# data.columns = c()),
# proteinGroups = list(identifier = c(),
# data.columns = c()),
)
# Match name
if (data.type %in% names(defaults)) {
return(defaults[[data.type]])
} else {
for (i in names(defaults)) {
if (regexpr(pattern = i, text = data.type) != -1) {
return(defaults[[i]])
}
}
}
return(list(identifier = NULL, data.columns = NULL))
}
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