diff --git a/R/processors.R b/R/processors.R index 925178a7..18393ec0 100644 --- a/R/processors.R +++ b/R/processors.R @@ -557,17 +557,18 @@ processElements <- function(d) { #' The fields of the output data.table are: #' #' \itemize{ -#' \item \code{gene.Symbol}: Symbol for the gene -#' \item \code{gene.Ensembl}: Ensembl ID for the gene +#' \item \code{gene.symbol}: Symbol for the gene +#' \item \code{gene.ensembl}: Ensembl ID for the gene #' \item \code{gene.NCBI}: NCBI id for the gene -#' \item \code{gene.Name}: Name of the gene -#' \item \code{gene.MFX.Rank}: Multifunctionality rank for the gene -#' \item \code{taxon.Name}: Name of the species -#' \item \code{taxon.Scientific}: Scientific name for the taxon +#' \item \code{gene.name}: Name of the gene +#' \item \code{gene.aliases}: Gene aliases. Each row includes a vector +#' \item \code{gene.MFX.rank}: Multifunctionality rank for the gene +#' \item \code{taxon.name}: Name of the species +#' \item \code{taxon.scientific}: Scientific name for the taxon #' \item \code{taxon.ID}: Internal identifier given to the species by Gemma #' \item \code{taxon.NCBI}: NCBI ID of the taxon -#' \item \code{taxon.Database.Name}: Underlying database used in Gemma for the taxon -#' \item \code{taxon.Database.ID}: ID of the underyling database used in Gemma for the taxon +#' \item \code{taxon.database.name}: Underlying database used in Gemma for the taxon +#' \item \code{taxon.database.ID}: ID of the underlying database used in Gemma for the taxon #' } #' #' @keywords internal @@ -577,6 +578,9 @@ processGenes <- function(d) { gene.ensembl = accessField(d,'ensemblId',NA_character_), gene.NCBI = accessField(d,"ncbiId",NA_integer_), gene.name = accessField(d, "officialName",NA_character_), + gene.aliases = d %>% purrr::map(function(x){ + x$aliases %>% unlist + }), # gene.Aliases = d[["aliases"]], # gene.GO = d[["numGoTerms"]], # gene.Homologues = d[["homologues"]], diff --git a/man/get_genes.Rd b/man/get_genes.Rd index 3450908e..89dbe484 100644 --- a/man/get_genes.Rd +++ b/man/get_genes.Rd @@ -38,17 +38,18 @@ A list if \code{raw = TRUE}. The fields of the output data.table are: \itemize{ -\item \code{gene.Symbol}: Symbol for the gene -\item \code{gene.Ensembl}: Ensembl ID for the gene +\item \code{gene.symbol}: Symbol for the gene +\item \code{gene.ensembl}: Ensembl ID for the gene \item \code{gene.NCBI}: NCBI id for the gene -\item \code{gene.Name}: Name of the gene -\item \code{gene.MFX.Rank}: Multifunctionality rank for the gene -\item \code{taxon.Name}: Name of the species -\item \code{taxon.Scientific}: Scientific name for the taxon +\item \code{gene.name}: Name of the gene +\item \code{gene.aliases}: Gene aliases. Each row includes a vector +\item \code{gene.MFX.rank}: Multifunctionality rank for the gene +\item \code{taxon.name}: Name of the species +\item \code{taxon.scientific}: Scientific name for the taxon \item \code{taxon.ID}: Internal identifier given to the species by Gemma \item \code{taxon.NCBI}: NCBI ID of the taxon -\item \code{taxon.Database.Name}: Underlying database used in Gemma for the taxon -\item \code{taxon.Database.ID}: ID of the underyling database used in Gemma for the taxon +\item \code{taxon.database.name}: Underlying database used in Gemma for the taxon +\item \code{taxon.database.ID}: ID of the underlying database used in Gemma for the taxon } } \description{ diff --git a/man/get_platform_element_genes.Rd b/man/get_platform_element_genes.Rd index dbacd176..60a7da9d 100644 --- a/man/get_platform_element_genes.Rd +++ b/man/get_platform_element_genes.Rd @@ -50,17 +50,18 @@ A list if \code{raw = TRUE}. The fields of the output data.table are: \itemize{ -\item \code{gene.Symbol}: Symbol for the gene -\item \code{gene.Ensembl}: Ensembl ID for the gene +\item \code{gene.symbol}: Symbol for the gene +\item \code{gene.ensembl}: Ensembl ID for the gene \item \code{gene.NCBI}: NCBI id for the gene -\item \code{gene.Name}: Name of the gene -\item \code{gene.MFX.Rank}: Multifunctionality rank for the gene -\item \code{taxon.Name}: Name of the species -\item \code{taxon.Scientific}: Scientific name for the taxon +\item \code{gene.name}: Name of the gene +\item \code{gene.aliases}: Gene aliases. Each row includes a vector +\item \code{gene.MFX.rank}: Multifunctionality rank for the gene +\item \code{taxon.name}: Name of the species +\item \code{taxon.scientific}: Scientific name for the taxon \item \code{taxon.ID}: Internal identifier given to the species by Gemma \item \code{taxon.NCBI}: NCBI ID of the taxon -\item \code{taxon.Database.Name}: Underlying database used in Gemma for the taxon -\item \code{taxon.Database.ID}: ID of the underyling database used in Gemma for the taxon +\item \code{taxon.database.name}: Underlying database used in Gemma for the taxon +\item \code{taxon.database.ID}: ID of the underlying database used in Gemma for the taxon } } \description{ diff --git a/man/processGenes.Rd b/man/processGenes.Rd index d726c9ae..d311ef77 100644 --- a/man/processGenes.Rd +++ b/man/processGenes.Rd @@ -16,17 +16,18 @@ A list if \code{raw = TRUE}. The fields of the output data.table are: \itemize{ -\item \code{gene.Symbol}: Symbol for the gene -\item \code{gene.Ensembl}: Ensembl ID for the gene +\item \code{gene.symbol}: Symbol for the gene +\item \code{gene.ensembl}: Ensembl ID for the gene \item \code{gene.NCBI}: NCBI id for the gene -\item \code{gene.Name}: Name of the gene -\item \code{gene.MFX.Rank}: Multifunctionality rank for the gene -\item \code{taxon.Name}: Name of the species -\item \code{taxon.Scientific}: Scientific name for the taxon +\item \code{gene.name}: Name of the gene +\item \code{gene.aliases}: Gene aliases. Each row includes a vector +\item \code{gene.MFX.rank}: Multifunctionality rank for the gene +\item \code{taxon.name}: Name of the species +\item \code{taxon.scientific}: Scientific name for the taxon \item \code{taxon.ID}: Internal identifier given to the species by Gemma \item \code{taxon.NCBI}: NCBI ID of the taxon -\item \code{taxon.Database.Name}: Underlying database used in Gemma for the taxon -\item \code{taxon.Database.ID}: ID of the underyling database used in Gemma for the taxon +\item \code{taxon.database.name}: Underlying database used in Gemma for the taxon +\item \code{taxon.database.ID}: ID of the underlying database used in Gemma for the taxon } } \description{