R/datasets.R

In oberstal/pfGO: Plasmodium falciparum functional enrichment analysis tools

## Pfal_geneID2GO_curated ----
#' @title All curated GO terms mapped to \emph{P. falciparum} genes
#' @name Pfal_geneID2GO_curated
#' @docType data
#' @description
#' A \emph{P. falciparum} GO database containing all curated GO terms mapped to \emph{P. falciparum} genes (from PlasmoDB release 66; accessed Sep 28, 2023).
#'
#' @usage data(Pfal_geneID2GO_curated)
#' @format A list of 3454 named vectors--one vector for each \emph{Pf} geneID to which GO terms are mapped. Each vector contains all curated GO-terms mapped to the geneID.
#' @source <https://plasmodb.org/common/downloads/Current_Release/Pfalciparum3D7/gaf/PlasmoDB-66_Pfalciparum3D7_GO.gaf.gzip>
#' @description Can be used as the geneID2GO input for run.topGO.meta.
#' @examples
#' run.topGO.meta(mydf = exampleMydf, geneID2GO = Pfal_geneID2GO_curated)
"Pfal_geneID2GO_curated"


## Pfal_geneID2GO ----
#' @title All GO terms mapped to \emph{P. falciparum} genes
#' @name Pfal_geneID2GO
#' @docType data
#' @description
#' A \emph{P. falciparum} GO database containing all GO terms mapped to \emph{P. falciparum} genes (from PlasmoDB release 66; accessed October 18, 2023). Includes automated annotations (evidence code "IEA").
#'
#' @usage data(Pfal_geneID2GO)
#' @format A list of 4477 named vectors--one vector for each \emph{Pf} geneID to which GO terms are mapped. Each vector contains all GO-terms mapped to the geneID.
#' @source <https://plasmodb.org/common/downloads/Current_Release/Pfalciparum3D7/gaf/PlasmoDB-66_Pfalciparum3D7_GO.gaf.gzip>
#' @description Can be used as the geneID2GO input for run.topGO.meta.
#' @examples
#' run.topGO.meta(mydf = exampleMydf, geneID2GO = Pfal_geneID2GO)
"Pfal_geneID2GO"





## exampleMydf ----
#' @title \emph{piggyBac} mutant classification-data from pooled 1k heat shock screen
#' @name exampleMydf
#' @docType data
#' @description
#' A data frame with \emph{P. falciparum} geneIDs in column 1, and interest-category classifications in column 2. In pooled \emph{piggyBac}-mutant screening, common interest-category classifications may be some form of "sensitive", "tolerant", and "neutral".
#'
#' All mutants detected above threshold in the pooled 1k-library heat shock screen are included in this table (n = 752). Derived from /url{https://www.nature.com/articles/s41467-021-24814-1}, Table S2.

#'
#' @usage data(exampleMydf)
#' @format A 2-column data frame with 752 \emph{P. falciparum} geneIDs in column 1, and interest-category classifications (here, phenotypes in pooled screening) in column 2.
#' @source <https://www.nature.com/articles/s41467-021-24814-1>
#' @description can be used as example mydf input for run.topGO.meta.
#' @examples
#' run.topGO.meta(mydf = exampleMydf, geneID2GO = Pfal_geneID2GO)
"exampleMydf"



## pf.annot ----
#' @title All \emph{P. falciparum} gene-product annotations.
#' @name pf.annot
#' @docType data
#'
#' @description
#' A dataset containing all \emph{P. falciparum} gene-product annotations taken directly from gff file(reference strain 3D7). Only "gene" entries are kept to remove redundancy.
#'
#' @usage data(pf.annot)
#'
#' @format A data frame of 5720 rows and 9 columns.
#'
#' \describe{
#'   \item{seqid}{chromosome ID.}
#'   \item{geneStart}{gene start coordinate.}
#'   \item{geneEnd}{gene end coordinate.}
#'   \item{strand}{gene strand.}
#'   \item{type}{type of annotation. Here protein-coding genes, ncRNA genes and pseudogenes are kept.}
#'   \item{geneID}{gene ID.}
#'   \item{description}{functional annotation.}
#'   \item{geneName}{the gene symbol, or short name, if one exists; otherwise the geneID is used.}
#'   \item{source}{annotation source.}
#' }
#'
#' @source <https://plasmodb.org/common/downloads/release-66/Pfalciparum3D7/gff/data/PlasmoDB-66_Pfalciparum3D7.gff>
#'
#' @keywords dataset
#' @details ## Keep in mind:
#' These data aren't explicitly required for running any enrichments with this package. They are included for reference to aid exploring your enrichment results.
#'
#' Some redundant columns were filtered/removed from the original data source.
#'
#' Updated versions can be generated using the \link{get.pfannot} function and specifying the url or filepath to your preferred plasmoDB .gff file. Note the run.topGO.meta function currently calls get.pfannot with plasmoDB release 66 to annotate the significant-genes-in-enriched-terms output.
#'
"pf.annot"


## pf.genesets.mpmp ----
#' @title Curated \emph{P. falciparum} gene-sets.
#' @name pf.genesets.mpmp
#' @docType data
#' @description
#' curated \emph{P. falciparum} metabolic pathways, gene-sets, GO terms from MPMP
#' @usage data(pf.genesets.mpmp)
#'
#' @format A large data frame of 54090 rows and 5 columns.
#'
#' \describe{
#'   \item{Gene.ID}{*P. falciparum* gene ID}
#'   \item{Map.Name}{name of the metabolic pathway map/other gene-set curated from publication; searchable at the MPMP website}
#'   \item{Map_id}{the mpmp website address for the pathway map if applicable/the mpmp page for that gene-set. Follow these links to view pathways of interest.)}
#'   \item{Map.cat}{appears to be the gene symbol (short name), or gene-product where available}
#'   \item{pla.id}{appears to be the GO term or enzyme-code where applicable/available}
#' }
#'
#' @source the Malaria Parasite Metabolic Pathways database (MPMP). <https://mpmp.huji.ac.il>
#'
#' @details Not sure about date of access or exact origins of this dataset, but shared from Chengqi Wang in April 2021.
"pf.genesets.mpmp"


## insertions ----
#' @title \emph{piggyBac} insertions reported in Zhang et al. 2018 (Science)
#' @name pf.insertions
#' @docType data
#' @description
#' \emph{P. falciparum} insertion-data as published in Science 2018. Contains 3 of the published supplemental tables (Table S1, pilot_library; Table S3, saturation_library; Table S5, genesbyMIS). Not needed to run GO enrichment functions, but useful additional info to have for interpreting output.
#'
#' @usage data(pf.insertions)
#' @format A list of 3 dataframes--pilot_library, corresponding to published table S1; saturation_library, corresponding to Table S3, and genesbyMIS, corresponding to Table S5. Column-names have been edited to be R-friendly.
#' @source <https://www.science.org/doi/10.1126/science.aap7847>

"pf.insertions"