R/data.R

In PhyloProfile: PhyloProfile

#' NCBI Taxonomy reduced data set
#' 
#' @docType data
#' @name taxonNamesReduced
#' @description A list of NCBI taxonomy info (including taxon IDs, taxon names, 
#' their systematic taxonomy rank and IDs of their next rank - parent IDs) for 
#' 95 taxa in two experimental sets included in PhyloProfilData package.
#' @format A data frame with 4 columns:
#' \itemize{
#'     \item{ncbiID}{ e.g. "10090"}
#'     \item{fullName}{ e.g. "Mus musculus"}
#'     \item{rank}{ e.g. "species"}
#'     \item{parentID}{ e.g. "862507"}
#' }
#' @usage data(taxonNamesReduced)
NULL

#' NCBI ID list for experimental data sets
#' 
#' @docType data
#' @name idList
#' @description Data frame, in which each row contains the complete taxonomy 
#' ranks from the lowest systematic level (strain/species) upto the taxonomy 
#' root and the corresponding IDs for one taxon in the experimental data sets.
#' @format A data frame with up to 41 columns and 95 rows corresponding to 95
#' taxa in the 2 experimental data sets
#' @usage data(idList)
NULL

#' NCBI rank list for experimental data sets
#'
#' @docType data
#' @name rankList
#' @description Data frame, in which each row contains the complete taxonomy 
#' ranks from the lowest systematic level (strain/species) upto the taxonomy 
#' root for one taxon in the experimental data sets.
#' @format A data frame with up to 41 columns and 95 rows corresponding to 95
#' taxa in the 2 experimental data sets
#' @usage data(rankList)
NULL

#' Taxonomy matrix for experimental data sets
#'
#' @docType data
#' @name taxonomyMatrix
#' @description Data frame containing the fully aligned taxonomy IDs of 95 taxa 
#' in the experimental data sets. By talking into account both the defined 
#' ranks (e.g. strain, This data is used for clustering and then creating a
#' taxon tree. It is used also for cross-linking between different taxonomy
#' ranks within a taxon.
#' @format A data frame with up to 147 columns and 95 rows corresponding to 95
#' taxa in the 2 experimental data sets
#' @usage data(taxonomyMatrix)
NULL

#' An example of a taxonomy tree in newick format.
#'
#' @docType data
#' @name ppTree
#' @format A data frame with only one entry
#' \describe{
#'     \item{V1}{ tree in newick format}
#' }
#' @usage data(ppTree)
NULL

#' An example of a taxonomy matrix.
#'
#' @docType data
#' @name ppTaxonomyMatrix
#' @format A data frame with 10 rows and 162 variables:
#' \itemize{
#'     \item{abbrName}{ e.g. "ncbi10090"}
#'     \item{ncbiID}{ e.g. "10090"}
#'     \item{fullName}{ e.g. "Mus musculus"}
#'     \item{strain}{ e.g. "10090"}
#'     ...
#' }
#' @usage data(ppTaxonomyMatrix)
NULL

#' An example of a raw long input file.
#'
#' @docType data
#' @name mainLongRaw
#' @format A data frame with 168 rows and 5 variables:
#' \itemize{
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "100136at6656"}
#'     \item{ncbiID}{ Taxon ID, e.g. "ncbi36329"}
#'     \item{orthoID}{ Ortholog ID, e.g. "100136at6656|PLAF7@36329@1|Q8ILT8|1"}
#'     \item{FAS_F}{ First additional variable}
#'     \item{FAS_B}{ Second additional variable}
#' }
#' @usage data(mainLongRaw)
NULL

#' An example of a raw long input file together with the taxonomy info.
#'
#' @docType data
#' @name profileWithTaxonomy
#' @format A data frame with 20 rows and 12 variables:
#' \itemize{
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "OG_1017"}
#'     \item{ncbiID}{ Taxon ID, e.g. "ncbi176299"}
#'     \item{orthoID}{ Ortholog ID, e.g. "A.fabrum@176299@1582"}
#'     \item{var1}{ First additional variable}
#'     \item{var2}{ Second additional variable}
#'     \item{paralog}{ Number of co-orthologs in the current taxon}
#'     \item{abbrName}{ e.g. "ncbi176299"}
#'     \item{taxonID}{ Taxon ID, e.g. "176299"}
#'     \item{fullName}{ Full taxon name, e.g. "Agrobacterium fabrum str. C58"}
#'     \item{supertaxonID}{ Supertaxon ID (only different than ncbiID in case
#'     working with higher taxonomy rank than input's)}
#'     \item{supertaxon}{ Name of the corresponding supertaxon}
#'     \item{rank}{ Rank of the supertaxon}
#' }
#' @usage data(profileWithTaxonomy)
NULL

#' An example of a fully processed phylogenetic profile.
#'
#' @docType data
#' @name fullProcessedProfile
#' @format A data frame with 168 rows and 16 variables:
#' \itemize{
#'     \item{supertaxon}{ Supertaxon name together with its ordered index, e.g.
#'     "1001_Mammalia"}
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "100136at6656"}
#'     \item{ncbiID}{ Taxon ID, e.g. "ncbi10116"}
#'     \item{orthoID}{ Ortholog ID, e.g. "100136at6656|HUMAN@9606@1|Q9UNQ2|1"}
#'     \item{var1}{ First additional variable}
#'     \item{var2}{ Second additional variable}
#'     \item{paralog}{ Number of co-orthologs in the current taxon}
#'     \item{abbrName}{ NCBI ID of the ortholog, e.g. "ncbi9606"}
#'     \item{taxonID}{ Taxon ID of the ortholog, in this case: "0"}
#'     \item{fullName}{ Full taxon name of the ortholog, e.g. "Homo sapiens"}
#'     \item{supertaxonID}{ Supertaxon ID (only different than ncbiID in case
#'     working with higher taxonomy rank than input's). e.g. "40674"}
#'     \item{rank}{ Rank of the supertaxon, e.g. "class"}
#'     \item{category}{ "cat}
#'     \item{mVar1}{ Value of the 1. variable after grouping into supertaxon}
#'     \item{mVar2}{ Value of the 2. variable after grouping into supertaxon}
#'     \item{numberSpec}{ Total number of species in each supertaxon}
#' }
#' @usage data(fullProcessedProfile)
NULL

#' An example of a filtered phylogenetic profile.
#'
#' @docType data
#' @name filteredProfile
#' @format A data frame with 168 rows and 18 variables:
#' \itemize{
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "100136at6656"}
#'     \item{supertaxon}{ Supertaxon name together with its ordered index, e.g.
#'     "1001_Mammalia"}
#'     \item{ncbiID}{ Taxon ID, e.g. "ncbi10116"}
#'     \item{orthoID}{ Ortholog ID, e.g. "100136at6656|HUMAN@9606@1|Q9UNQ2|1"}
#'     \item{var1}{ First additional variable}
#'     \item{var2}{ Second additional variable}
#'     \item{paralog}{ Number of co-orthologs in the current taxon}
#'     \item{abbrName}{ NCBI ID of the ortholog, e.g. "ncbi9606"}
#'     \item{taxonID}{ Taxon ID of the ortholog, in this case: "0"}
#'     \item{fullName}{ Full taxon name of the ortholog, e.g. "Homo sapiens"}
#'     \item{supertaxonID}{ Supertaxon ID (only different than ncbiID in case
#'     working with higher taxonomy rank than input's). e.g. "40674"}
#'     \item{rank}{ Rank of the supertaxon, e.g. "class"}
#'     \item{category}{ "cat}
#'     \item{mVar1}{ Value of the 1. variable after grouping into supertaxon}
#'     \item{mVar2}{ Value of the 2. variable after grouping into supertaxon}
#'     \item{numberSpec}{ Total number of species in each supertaxon}
#'     \item{taxonMod}{ Name of supersupertaxon w/o its index, e.g. "Mammalia"}
#'     \item{presSpec}{ Percentage of taxa that have ortho in each supertaxon}
#' }
#' @usage data(filteredProfile)
NULL

#' An example of a final phylogenetic profile in supertaxon level.
#'
#' @docType data
#' @name superTaxonProfile
#' @format A data frame with 91 rows and 9 variables:
#' \itemize{
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "100136at6656"}
#'     \item{supertaxon}{ Supertaxon name together with its ordered index, e.g.
#'     "1001_Mammalia"}
#'     \item{supertaxonID}{ Supertaxon ID (only different than ncbiID in case
#'     working with higher taxonomy rank than input's). e.g. "40674"}
#'     \item{var1}{ First additional variable}
#'     \item{presSpec}{ Percentage of taxa that have ortho in each supertaxon}
#'     \item{category}{ "cat}
#'     \item{orthoID}{ Ortholog ID, e.g. "100136at6656|HUMAN@9606@1|Q9UNQ2|1"}
#'     \item{var2}{ Second additional variable}
#'     \item{paralog}{ Number of co-orthologs in the current taxon}
#' }
#' @usage data(superTaxonProfile)
NULL

#' An example of a final processed & filtered phylogenetic profile.
#'
#' @docType data
#' @name finalProcessedProfile
#' @format A data frame with 91 rows and 10 variables:
#' \itemize{
#'     \item{geneID}{ Seed or ortholog group ID, e.g. "100136at6656"}
#'     \item{supertaxon}{ Supertaxon name together with its ordered index, e.g.
#'     "1001_Mammalia"}
#'     \item{supertaxonID}{ Supertaxon ID (only different than ncbiID in case
#'     working with higher taxonomy rank than input's). e.g. "40674"}
#'     \item{var1}{ First additional variable}
#'     \item{presSpec}{ The percentage of species presenting in each supertaxon}
#'     \item{category}{ "cat"}
#'     \item{orthoID}{ Ortholog ID, e.g. "100136at6656|RAT@10116@1|G3V7R8|1"}
#'     \item{var2}{ Second additional variable}
#'     \item{paralog}{ Number of co-orthologs in the current taxon}
#'     \item{taxonMon}{ Name of supertaxon but without index, e.g. "Mammalia"}
#' }
#' @usage data(finalProcessedProfile)
NULL