@@ -1,5 +1,8 @@

 #' Get functional term data from BioPlanet

 #'

+#' Download term information (term ID and name) and gene-pathway mapping

+#' (NCBI gene ID, gene symbol and pathway ID) from BioPlanet.

+#'

 #' @return A list with \code{terms} and \code{mapping} tibbles.

 #' @export

 #'

@@ -16,12 +16,12 @@

 #' @param mapping Information about term-feature mapping. A tibble with

 #'   \code{term_id} and a feature id, as identified with \code{feature_name}

 #'   argument. For example, if this tibble contains \code{gene_symbol} and

-#'   \code{term_id}, then \code{feature_name = "gene_symbol"}.

+#'   \code{term_id}, then you need to set \code{feature_name = "gene_symbol"}.

 #' @param all_features A vector with all feature ids used as background for

-#'   enrichment. If not specified, all features from \code{mapping} will be

-#'   used, resulting in a larger objects size.

+#'   enrichment. If not specified, all features found in \code{mapping} will be

+#'   used, resulting in a larger object size.

 #' @param feature_name Which column to use from mapping table, e.g.

-#'   "gene_symbol" or "ensembl_gene_id".

+#'   \code{gene_symbol} or \code{ensembl_gene_id}.

 #'

 #' @return An object class \code{fenr_terms} required by

 #'   \code{functional_enrichment}.

@@ -98,18 +98,18 @@ prepare_for_enrichment <- function(terms, mapping, all_features = NULL, feature_

 #' @details

 #'

 #' Functional enrichment in a selection (e.g. significantly DE features) of

-#' features, using hypergeometric probability. A feature can be a gene, protein,

-#' etc. `term_data` is an object with functional term information and

-#' feature-term assignment. It is a list of: `term2info` - a named vector term

-#' id => term name; `term2feature` - a list term_id => vector of feature_ids;

-#' `feature2term` - a list feature id => vector of term ids. It can be created

-#' by `prepare_for_enrichment` function.

+#' features, using hypergeometric probability (that is Fisher's exact test). A

+#' feature can be a gene, protein, etc. \code{term_data} is an object with

+#' functional term information and feature-term assignment.

 #'

 #' @param feat_all A character vector with all feature identifiers. This is the

 #'   background for enrichment.

 #' @param feat_sel A character vector with feature identifiers in the selection.

-#' @param term_data An object class \code{fenr_terms}, as explained in details.

-#'   It can be created using \code{prepare_for_enrichment}.

+#' @param term_data An object class \code{fenr_terms}, created by

+#'   \code{prepare_for_enrichment}. It is a list of three elements: \itemize{

+#'   \item{\code{term2info} - a named vector term id => term name}

+#'   \item{\code{term2feature} - a list term id => vector of feature ids}

+#'   \item{\code{feature2term} - a list feature id => vector of term ids}}

 #' @param feat2name An optional named list to convert feature id into feature

 #'   name.

 #' @param min_count Minimal count of features with term in the selection to be

@@ -117,14 +117,16 @@ prepare_for_enrichment <- function(terms, mapping, all_features = NULL, feature_

 #' @param fdr_limit Only terms with p_adjust below this limit are returned.

 #'

 #' @return A tibble with enrichment results. For each term the following

-#'   quantities are reported: N_with - number of features with this term in the

-#'   among all features, n_with_sel - number of features with this term in the

-#'   selection, n_expect - expected number of features with this term in the

-#'   selection, under the null hypothesis that terms are assigned to features

-#'   randomly, enrichment - ratio of n_with_sel / n_expect; odds_ratio - odds

-#'   ratio for enrichment, p_value - p-value from a single hypergeometric test;

-#'   p_adjust - p-value adjusted for multiple tests using Benjamini-Hochberg

-#'   approach.

+#'   quantities are reported: \itemize{ \item{\code{N_with} - number of features

+#'   with this term in the among all features} \item{\code{n_with_sel} - number of

+#'   features with this term in the selection} \item{\code{n_expect} - expected

+#'   number of features with this term in the selection, under the null

+#'   hypothesis that terms are assigned to features randomly}

+#'   \item{\code{enrichment} - ratio of n_with_sel / n_expect}

+#'   \item{\code{odds_ratio} - odds ratio for enrichment; is infinite, when all

+#'   features with the given term are in the selection} \item{\code{p_value} -

+#'   p-value from a single hypergeometric test} \item{\code{p_adjust} - p-value

+#'   adjusted for multiple tests using Benjamini-Hochberg approach} }

 #'

 #' @examples

 #' bp <- fetch_bp()

@@ -4,9 +4,9 @@

 #' gene ID, gene symbol and pathway ID) from KEGG. Gene symbols are extracted

 #' from gene descriptions. For some species (e.g. yeast), gene symbols are

 #' returned instead of entrez IDs and not in gene description. This function is

-#' based on BioConductor package \code{KEGGREST}.

+#' based on BioConductor package \pkg{KEGGREST}.

 #'

-#' @param species KEGG species code, for example \code{"hsa"} for human. The

+#' @param species KEGG species code, for example "hsa" for human. The

 #'   full list of available KEGG species can be found by using

 #'   \code{KEGGREST::keggList("organism")}. The column \code{organism} contains

 #'   the codes used here.

@@ -2,7 +2,7 @@

 #'

 #' @param spec Reactome species

 #'

-#' @return A tibble with \code{term_id} and \code{term_name}

+#' @return A tibble with columns \code{term_id} and \code{term_name}

 fetch_reactome_pathways <- function(spec) {

   url <- "https://reactome.org/download/current/ReactomePathways.txt"

   colms <- c("term_id", "term_name", "species")

@@ -14,7 +14,7 @@ fetch_reactome_pathways <- function(spec) {

 #'

 #' @param spec Reactome species

 #'

-#' @return A tibble with \code{gene_id} and \code{term_id}

+#' @return A tibble with columns \code{gene_id} and \code{term_id}

 fetch_reactome_ensembl_genes <- function(spec) {

   url <- "https://reactome.org/download/current/Ensembl2Reactome.txt"

   colms <- c("gene_id", "term_id", "url", "event", "evidence", "species")

@@ -26,7 +26,7 @@ fetch_reactome_ensembl_genes <- function(spec) {

 #' List of available Reactome species

 #'

-#' @return A character vector with species names used by Reactome

+#' @return A character vector with species names used by Reactome.

 #' @export

 fetch_reactome_species <- function() {

   url <- "https://reactome.org/download/current/Ensembl2Reactome.txt"

@@ -41,8 +41,8 @@ fetch_reactome_species <- function() {

 #' Download term information (pathway ID and name) and gene-pathway mapping

 #' (Ensembl gene ID and pathway ID) from Reactome.

 #'

-#' @param species Reactome species designation, for example \code{"Homo

-#'   sapiens"} for human. Full list of available species can be found using

+#' @param species Reactome species designation, for example "Homo

+#'   sapiens" for human. Full list of available species can be found using

 #'   \code{fetch_reactome_species()}.

 #'

 #' @return A list with \code{terms} and \code{mapping} tibbles.

@@ -1,6 +1,6 @@

 #' Check if URL file exists

 #'

-#' From https://stackoverflow.com/questions/52911812/check-if-url-exists-in-r.

+#' From \url{https://stackoverflow.com/questions/52911812/check-if-url-exists-in-r}.

 #

 #' @param x a single URL

 #' @param non_2xx_return_value what to do if the site exists but the

@@ -10,7 +10,8 @@ fetch_bp()

 A list with \code{terms} and \code{mapping} tibbles.

 }

 \description{

-Get functional term data from BioPlanet

+Download term information (term ID and name) and gene-pathway mapping

+(NCBI gene ID, gene symbol and pathway ID) from BioPlanet.

 }

 \examples{

 \dontrun{

@@ -7,9 +7,9 @@

 fetch_go_from_go(species)

 }

 \arguments{

-\item{species}{Root name for species file under

-\code{http://current.geneontology.org/annotations}. Examples are

-\code{"goa_human"} for human, \code{"mgi"} for mouse or \code{"sgd"} for yeast.}

+\item{species}{Species designation. Base file name for species file under

+\url{http://current.geneontology.org/annotations}. Examples are

+\file{goa_human} for human, \file{mgi} for mouse or \file{sgd} for yeast.}

 }

 \value{

 A list with \code{terms} and \code{mapping} tibbles.

@@ -11,7 +11,8 @@ fetch_go_genes_bm(mart)

 database, created with, e.g., \code{useEnsembl}.}

 }

 \value{

-A tibble with ensembl_gene_is, gene_symbol and term_id.

+A tibble with columns \code{ensembl_gene_id}, \code{gene_symbol} and

+  \code{term_id}.

 }

 \description{

 Download GO term gene mapping from Ensembl

@@ -7,12 +7,12 @@

 fetch_go_genes_go(species)

 }

 \arguments{

-\item{species}{Root name for species file under

-\code{http://current.geneontology.org/annotations}. Examples are

-\code{goa_human} for human, \code{mgi} for mouse or \code{sgd} for yeast.}

+\item{species}{Species designation. Base file name for species file under

+\url{http://current.geneontology.org/annotations}. Examples are

+\file{goa_human} for human, \file{mgi} for mouse or \file{sgd} for yeast.}

 }

 \value{

-A tibble with gene_name, uniprot_id and term_id.

+A tibble with columns \code{gene_symbol}, \code{uniprot_id} and \code{term_id}.

 }

 \description{

 Download GO term gene mapping from geneontology.org

@@ -7,7 +7,7 @@

 fetch_kegg(species, batch_size = 10)

 }

 \arguments{

-\item{species}{KEGG species code, for example \code{"hsa"} for human. The

+\item{species}{KEGG species code, for example "hsa" for human. The

 full list of available KEGG species can be found by using

 \code{KEGGREST::keggList("organism")}. The column \code{organism} contains

 the codes used here.}

@@ -23,7 +23,7 @@ Download information (pathway ID and name) and gene-pathway mapping (entrez

 gene ID, gene symbol and pathway ID) from KEGG. Gene symbols are extracted

 from gene descriptions. For some species (e.g. yeast), gene symbols are

 returned instead of entrez IDs and not in gene description. This function is

-based on BioConductor package \code{KEGGREST}.

+based on BioConductor package \pkg{KEGGREST}.

 }

 \examples{

 \dontrun{

@@ -7,8 +7,8 @@

 fetch_reactome(species)

 }

 \arguments{

-\item{species}{Reactome species designation, for example \code{"Homo

-sapiens"} for human. Full list of available species can be found using

+\item{species}{Reactome species designation, for example "Homo

+sapiens" for human. Full list of available species can be found using

 \code{fetch_reactome_species()}.}

 }

 \value{

@@ -10,7 +10,7 @@ fetch_reactome_ensembl_genes(spec)

 \item{spec}{Reactome species}

 }

 \value{

-A tibble with \code{gene_id} and \code{term_id}

+A tibble with columns \code{gene_id} and \code{term_id}

 }

 \description{

 Download term Ensembl gene ID mapping from Reactome

@@ -10,7 +10,7 @@ fetch_reactome_pathways(spec)

 \item{spec}{Reactome species}

 }

 \value{

-A tibble with \code{term_id} and \code{term_name}

+A tibble with columns \code{term_id} and \code{term_name}

 }

 \description{

 Download pathway data from Reactome

@@ -7,7 +7,7 @@

 fetch_reactome_species()

 }

 \value{

-A character vector with species names used by Reactome

+A character vector with species names used by Reactome.

 }

 \description{

 List of available Reactome species

@@ -19,8 +19,11 @@ background for enrichment.}

 \item{feat_sel}{A character vector with feature identifiers in the selection.}

-\item{term_data}{An object class \code{fenr_terms}, as explained in details.

-It can be created using \code{prepare_for_enrichment}.}

+\item{term_data}{An object class \code{fenr_terms}, created by

+\code{prepare_for_enrichment}. It is a list of three elements: \itemize{

+\item{\code{term2info} - a named vector term id => term name}

+\item{\code{term2feature} - a list term id => vector of feature ids}

+\item{\code{feature2term} - a list feature id => vector of term ids}}}

 \item{feat2name}{An optional named list to convert feature id into feature

 name.}

@@ -32,14 +35,16 @@ used.}

 }

 \value{

 A tibble with enrichment results. For each term the following

-  quantities are reported: N_with - number of features with this term in the

-  among all features, n_with_sel - number of features with this term in the

-  selection, n_expect - expected number of features with this term in the

-  selection, under the null hypothesis that terms are assigned to features

-  randomly, enrichment - ratio of n_with_sel / n_expect; odds_ratio - odds

-  ratio for enrichment, p_value - p-value from a single hypergeometric test;

-  p_adjust - p-value adjusted for multiple tests using Benjamini-Hochberg

-  approach.

+  quantities are reported: \itemize{ \item{\code{N_with} - number of features

+  with this term in the among all features} \item{\code{n_with_sel} - number of

+  features with this term in the selection} \item{\code{n_expect} - expected

+  number of features with this term in the selection, under the null

+  hypothesis that terms are assigned to features randomly}

+  \item{\code{enrichment} - ratio of n_with_sel / n_expect}

+  \item{\code{odds_ratio} - odds ratio for enrichment; is infinite, when all

+  features with the given term are in the selection} \item{\code{p_value} -

+  p-value from a single hypergeometric test} \item{\code{p_adjust} - p-value

+  adjusted for multiple tests using Benjamini-Hochberg approach} }

 }

 \description{

 Fast functional enrichment based on hypergeometric distribution. Can be used

@@ -47,12 +52,9 @@ in interactive applications.

 }

 \details{

 Functional enrichment in a selection (e.g. significantly DE features) of

-features, using hypergeometric probability. A feature can be a gene, protein,

-etc. `term_data` is an object with functional term information and

-feature-term assignment. It is a list of: `term2info` - a named vector term

-id => term name; `term2feature` - a list term_id => vector of feature_ids;

-`feature2term` - a list feature id => vector of term ids. It can be created

-by `prepare_for_enrichment` function.

+features, using hypergeometric probability (that is Fisher's exact test). A

+feature can be a gene, protein, etc. \code{term_data} is an object with

+functional term information and feature-term assignment.

 }

 \examples{

 bp <- fetch_bp()

@@ -18,17 +18,17 @@ prepare_for_enrichment(

 \item{mapping}{Information about term-feature mapping. A tibble with

 \code{term_id} and a feature id, as identified with \code{feature_name}

 argument. For example, if this tibble contains \code{gene_symbol} and

-\code{term_id}, then \code{feature_name = "gene_symbol"}.}

+\code{term_id}, then you need to set \code{feature_name = "gene_symbol"}.}

 \item{all_features}{A vector with all feature ids used as background for

-enrichment. If not specified, all features from \code{mapping} will be

-used, resulting in a larger objects size.}

+enrichment. If not specified, all features found in \code{mapping} will be

+used, resulting in a larger object size.}

 \item{feature_name}{Which column to use from mapping table, e.g.

-"gene_symbol" or "ensembl_gene_id".}

+\code{gene_symbol} or \code{ensembl_gene_id}.}

 }

 \value{

-An object class \code{fterms} required by

+An object class \code{fenr_terms} required by

   \code{functional_enrichment}.

 }

 \description{

@@ -19,5 +19,5 @@ arises a warning message will be displayed. Default is `FALSE`.}

 to `httr::HEAD()` and/or `httr::GET()`}

 }

 \description{

-From https://stackoverflow.com/questions/52911812/check-if-url-exists-in-r.

+From \url{https://stackoverflow.com/questions/52911812/check-if-url-exists-in-r}.

 }