diff --git a/NAMESPACE b/NAMESPACE index 16e9640..3b5d65a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,6 +2,7 @@ export(ClusterORA) export(DMA) +export(EquivalentIDs) export(LoadGaude) export(LoadHallmarks) export(LoadKEGG) @@ -31,11 +32,14 @@ export(metaproviz_config_path) export(metaproviz_load_config) export(metaproviz_reset_config) export(metaproviz_save_config) +importFrom(KEGGREST,keggGet) +importFrom(KEGGREST,keggList) importFrom(OmnipathR,ambiguity) importFrom(OmnipathR,config_path) importFrom(OmnipathR,id_types) importFrom(OmnipathR,load_config) importFrom(OmnipathR,logfile) +importFrom(OmnipathR,ramp_table) importFrom(OmnipathR,read_log) importFrom(OmnipathR,reset_config) importFrom(OmnipathR,save_config) @@ -134,6 +138,7 @@ importFrom(purrr,map_int) importFrom(purrr,partial) importFrom(purrr,reduce) importFrom(qcc,mqcc) +importFrom(rappdirs,user_cache_dir) importFrom(readr,cols) importFrom(readr,read_csv) importFrom(reshape2,melt) @@ -154,6 +159,7 @@ importFrom(stats,lm) importFrom(stats,p.adjust) importFrom(stats,shapiro.test) importFrom(stringr,str_match) +importFrom(stringr,str_remove) importFrom(stringr,str_sub) importFrom(stringr,str_to_lower) importFrom(stringr,str_trim) diff --git a/man/EquivalentIDs.Rd b/man/EquivalentIDs.Rd new file mode 100644 index 0000000..5cb1c00 --- /dev/null +++ b/man/EquivalentIDs.Rd @@ -0,0 +1,44 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/RefactorPriorKnoweldge.R +\name{EquivalentIDs} +\alias{EquivalentIDs} +\title{Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb"} +\usage{ +EquivalentIDs( + InputData, + SettingsInfo = c(InputID = "MetaboliteID"), + From = "kegg", + SaveAs_Table = "csv", + FolderPath = NULL +) +} +\arguments{ +\item{InputData}{Dataframe with at least one column with the detected metabolite IDs (one ID per row).} + +\item{SettingsInfo}{\emph{Optional: } Column name of metabolite IDs. \strong{Default = list(InputID="MetaboliteID")}} + +\item{From}{ID type that is present in your data. Choose between "kegg", "pubchem", "chebi", "hmdb". \strong{Default = "kegg"}} + +\item{SaveAs_Table}{\emph{Optional: } File types for the analysis results are: "csv", "xlsx", "txt". \strong{Default = "csv"}} + +\item{FolderPath}{{Optional:} Path to the folder the results should be saved at. \strong{Default = NULL}} +} +\value{ +Input DF with additional column including potential additional IDs. +} +\description{ +Find additional potential IDs for "kegg", "pubchem", "chebi", "hmdb" +} +\examples{ +DetectedIDs <- MetaProViz::ToyData(Data="Cells_MetaData")\%>\% tibble::rownames_to_column("TrivialName")\%>\%tidyr::drop_na() +Res <- MetaProViz::EquivalentIDs(InputData= DetectedIDs, SettingsInfo = c(InputID="KEGG.ID"), From = "kegg") + +} +\keyword{Find} +\keyword{IDs} +\keyword{additional} +\keyword{for} +\keyword{identifier} +\keyword{metabolite} +\keyword{one} +\keyword{potential} diff --git a/man/LoadRAMP.Rd b/man/LoadRAMP.Rd index 209f26f..eb42a29 100644 --- a/man/LoadRAMP.Rd +++ b/man/LoadRAMP.Rd @@ -17,5 +17,9 @@ LoadRAMP(version = "2.5.4", SaveAs_Table = "csv", FolderPath = NULL) A data frame containing the Prior Knowledge. } \description{ -Import and process .csv file to create Prior Knowledge. +Import and process file to create Prior Knowledge. +} +\examples{ +ChemicalClass <- MetaProViz::LoadRAMP() + } diff --git a/man/ToyData.Rd b/man/ToyData.Rd index 61e39bd..55c5e5f 100644 --- a/man/ToyData.Rd +++ b/man/ToyData.Rd @@ -18,6 +18,8 @@ ToyData(Dataset) \item{\code{"Tissue_DMA"}: } \item{\code{"Tissue_DMA_Old"}: } \item{\code{"Tissue_DMA_Young"}: } +\item{\code{"Tissue_TvN_Proteomics"}: } +\item{\code{"Tissue_TvN_RNAseq"}: } }} } \value{ @@ -27,6 +29,6 @@ A data frame containing the toy data. Import and process .csv file to create toy data DF. } \examples{ -Intra <- ToyData("IntraCells_Raw") +Intra <- MetaProViz::ToyData("IntraCells_Raw") }