update docu

R/divergence_stratigraphy.R

@@ -139,7 +139,7 @@
 #'  
 #' @return A data.table storing the divergence map of the query organism.
 #' @seealso \code{\link{dNdS}}, \code{\link{divergence_map}},  \code{\link{substitutionrate}}, \code{\link{multi_aln}},
-#'   \code{\link{codon_aln}}, \code{\link{blast_best}}, \code{\link{blast_rec}}, \code{\link{map.generator}}
+#'   \code{\link{codon_aln}}, \code{\link{blast_best}}, \code{\link{blast_rec}}, \code{\link{map_generator_dnds}}
 #' @export
 divergence_stratigraphy <- function(query_file, 
                                     subject_file, 

R/filter_core_set.R

@@ -1,4 +1,8 @@
 #' @title Helper function to extract a core set of orthologous gene loci
+#' @description Helper function to extract a core set of orthologous gene loci
+#' @param x input data in \code{data.frame} or \code{tibble} format.
+#' @param order_species a character vector containing the scientific names of the organisms of interest
+#' ordered according to their phylogenetic distance to their reference species.  
 filter_core_set <- function(x, order_species) {
 
         subset_species <- sort(as.character(names(table(

R/filter_core_set_lnc.R

@@ -1,4 +1,8 @@
 #' @title Helper function to extract a core set of orthologous lncRNAs
+#' @description Helper function to extract a core set of orthologous lncRNAs.
+#' @param x input data in \code{data.frame} or \code{tibble} format.
+#' @param order_species a character vector containing the scientific names of the organisms of interest
+#' ordered according to their phylogenetic distance to their reference species. 
 filter_core_set_lnc <- function(x, order_species) {
 
         subset_species <- sort(as.character(names(table(

R/lnc_map_core_orthologs.R

@@ -1,7 +1,7 @@
 #' @title Retrieve a core set of orthologous lncRNAs from the pairwise lncRNA orthologs map
 #' @description Given a lnc_map table generated with \code{\link{map_generator_lnc}},
 #' this function will determine a core set of lncRNA orthologs that are shared between all species.
-#' @param ortho_tables a \code{lnc_map} that was generated with \code{\link{map_generator_lnc}}.
+#' @param lnc_map a \code{lnc_map} that was generated with \code{\link{map_generator_lnc}}.
 #' @param species_order a character string specifying species names listed in the order of phylogenetic/taxonomic distance from the query species.
 #' The species names must match with the species names present in the \code{lnc_map}.
 #' @author Hajk-Georg Drost

R/orthologs.R

@@ -44,15 +44,8 @@
 #' @author Hajk-Georg Drost
 #' @return A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes
 #' in the second column and the amino acid sequences in the third column.
-#' @references
-#' 
-#' BLAST: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
-#' 
-#' ProteinOrtho: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
-#'
 #' @examples \dontrun{
 #' 
-#' 
 #' ### BLAST Best Hit
 #' 
 #' # perform orthology inference using BLAST best hit
@@ -79,9 +72,6 @@
 #'           seq_type        = "protein", 
 #'           ortho_detection = "RBH", 
 #'           comp_cores      = 2)          
-#'           
-#'           
-#'           
 #' }
 #' @seealso \code{\link{blast_rec}}, \code{\link{dNdS}}
 #' @export

R/promotor_divergence_estimation.R

@@ -1,8 +1,8 @@
 #' @title Estimate the DNA distance between promotor sequences
 #' @description Given two \code{fasta} files storing the promotor sequence
 #' of protein coding genes, this function estimates the pairwise DNA distance between these promotor sequences.
-#' @param query file path to a query \code{fasta} file storing promotor sequences of interest (e.g. generated with \code{\link[metablastr]{extract_promotor_seqs_from_genome}}).
-#' @param subject file path to a subject \code{fasta} file storing promotor sequences of interest (e.g. generated with \code{\link[metablastr]{extract_promotor_seqs_from_genome}}).
+#' @param query file path to a query \code{fasta} file storing promotor sequences of interest (e.g. generated with \code{\link[metablastr]{extract_upstream_promotor_seqs}}).
+#' @param subject file path to a subject \code{fasta} file storing promotor sequences of interest (e.g. generated with \code{\link[metablastr]{extract_upstream_promotor_seqs}}).
 #' @param model a model as specified in \code{\link[ape]{dist.dna}}: a character string specifying the evolutionary model to be used - must be one of:
 #' \itemize{
 #' \item  \code{K80} (the default)

R/promotor_divergence_of_orthologous_genes.R

@@ -3,7 +3,7 @@
 #' from a set of pairwise species comparisons. It allows to add this promotor divergence information
 #' to an pre-computed \code{dNdS table} generated with \code{\link{dNdS}} or \code{\link{generate_ortholog_tables_all}}.
 #' @param promotor_folder a path to a folder containing promotor sequences in \code{fasta} format that
-#' were generated with \code{\link[metablastr]{extract_promotor_seqs_from_genome}}. 
+#' were generated with \code{\link[metablastr]{extract_upstream_promotor_seqs}}. 
 #' @param ortholog_tables_folder a path to a folder containing dNdS tables generated with \code{\link{generate_ortholog_tables_all}}
 #' @param model a model as specified in \code{\link[ape]{dist.dna}}: a character string specifying the evolutionary model to be used - must be one of:
 #' \itemize{
@@ -158,7 +158,7 @@ promotor_divergence_of_orthologous_genes <-
                                         unlist(stringr::str_split(x, "_"))[1]))
 
                         qry_matched_genes <-
-                                promotor_file_qry_sequences@ranges@NAMES[na.omit(
+                                promotor_file_qry_sequences@ranges@NAMES[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables$query_gene_locus_id,
                                                 promotor_file_qry_sequences@ranges@NAMES
@@ -198,7 +198,7 @@ promotor_divergence_of_orthologous_genes <-
                                           ))
 
                         sbj_matched_genes <-
-                                promotor_file_sbj_sequences@ranges@NAMES[na.omit(
+                                promotor_file_sbj_sequences@ranges@NAMES[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables$subject_gene_locus_id,
                                                 promotor_file_sbj_sequences@ranges@NAMES
@@ -244,28 +244,28 @@ promotor_divergence_of_orthologous_genes <-
                                         " orthologous genes were retained."
                                 )
 
-                                Biostrings::writeXStringSet(promotor_file_qry_sequences[na.omit(
+                                Biostrings::writeXStringSet(promotor_file_qry_sequences[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables_subset$query_gene_locus_id,
                                                 promotor_file_qry_sequences@ranges@NAMES
                                         )
                                 )], qry_output_file_path)
 
-                                Biostrings::writeXStringSet(promotor_file_sbj_sequences[na.omit(
+                                Biostrings::writeXStringSet(promotor_file_sbj_sequences[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables_subset$subject_gene_locus_id,
                                                 promotor_file_sbj_sequences@ranges@NAMES
                                         )
                                 )], sbj_output_file_path)
                         } else {
-                                Biostrings::writeXStringSet(promotor_file_qry_sequences[na.omit(
+                                Biostrings::writeXStringSet(promotor_file_qry_sequences[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables$query_gene_locus_id,
                                                 promotor_file_qry_sequences@ranges@NAMES
                                         )
                                 )], qry_output_file_path)
 
-                                Biostrings::writeXStringSet(promotor_file_sbj_sequences[na.omit(
+                                Biostrings::writeXStringSet(promotor_file_sbj_sequences[stats::na.omit(
                                         match(
                                                 species_specific_ortholog_tables$subject_gene_locus_id,
                                                 promotor_file_sbj_sequences@ranges@NAMES

R/set_blast.R

@@ -41,7 +41,7 @@
 #'  # running the set function to see an example output
 #'  head(set_blast(file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'))[[1]] , 2)
 #' }
-#' @seealso \code{\link{blast_best}}, \code{\link{blast_rec}}, \code{\link{advanced_blast}}, \code{\link{blast}}, \code{\link{advanced_makedb}}
+#' @seealso \code{\link{blast_best}}, \code{\link{blast_rec}}, \code{\link{blast}}
 #' @import data.table
 #' @export
 

R/testCoreOrthoParamsGeneLocus.R

@@ -1,4 +1,8 @@
-#' @title Helper function for plot_diverse_homology_thresholds_core_orthologs
+#' @title Helper function for \code{plot_diverse_homology_thresholds_core_orthologs}
+#' @description Helper function for \code{\link{plot_diverse_homology_thresholds_core_orthologs}}.
+#' @param ortho_tables a \code{ortho tables} that was generated with \code{\link{generate_ortholog_tables_all}}.
+#' @param param parameters.
+#' @param species_order a character string specifying species names listed in the order of phylogenetic/taxonomic distance from the query species.
 testCoreOrthoParamsGeneLocus <-
         function(ortho_tables, param, species_order) {
                 ortho_tables_core <-

R/testCoreOrthoParamsSplicceVariant.R

@@ -1,4 +1,10 @@
-#' @title Helper function for plot_diverse_homology_thresholds_core_orthologs 2
+#' @title Helper function for splice variant based \code{plot_diverse_homology_thresholds_core_orthologs}
+#' @description Helper function for splice variant based \code{\link{plot_diverse_homology_thresholds_core_orthologs}}.
+#' @param ortho_tables a \code{ortho tables} that was generated with \code{\link{generate_ortholog_tables_all}}.
+#' @param param parameters.
+#' @param species_order a character string specifying species names listed in the order of phylogenetic/taxonomic distance from the query species.
+#' @param n_core_species number of core species.
+
 testCoreOrthoParamsSpliceVariant <-
         function(ortho_tables,
                  param,

R/translate_cds_to_protein.R

@@ -7,7 +7,7 @@
 #' shall be stored as \code{fasta} file.
 #' @param delete_corrupt_cds delete_corrupt_cds a logical value indicating whether sequences with corrupt base triplets should be removed from the input \code{file}. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.
 #' @author Hajk-Georg Drost
-#' @examples dontrun{
+#' @examples \dontrun{
 #' # install.packages("biomartr")
 #' # download coding sequences of Arabidopsis thaliana
 #' Ath_file_path <- biomartr::getCDS(db = "refseq",

R/translate_cds_to_protein_all.R

@@ -6,7 +6,7 @@
 #' @param output_folder name or file path to a folder that that shall be generated to store the output \code{fasta} files.
 #' @param delete_corrupt_cds delete_corrupt_cds a logical value indicating whether sequences with corrupt base triplets should be removed from the input \code{file}. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.
 #' @author Hajk-Georg Drost
-#' @examples dontrun{
+#' @examples \dontrun{
 #' # install.packages("biomartr")
 #' # download coding sequences of Arabidopsis thaliana, Arabidopsis lyrata, and Capsella rubella
 #' org_list <- c("Arabidopsis thaliana", "Arabidopsis lyrata", "Capsella rubella")