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lnc_map_counts.R
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lnc_map_counts.R
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#' @title Count number of orthologous lncRNAs per pairwise species comparison
#' @description This function takes a orthologous lncRNA map generated with \code{\link{map_generator_lnc}}
#' as input and groups the table by species to count the number of orthologous lncRNAs per pairwise species comparison
#' using the reference (query) species specified in \code{\link{map_generator_lnc}}.
#' @param lnc_map a orthologous lncRNA map generated with \code{\link{map_generator_lnc}}.
#' @param species_order 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 \code{map_generator_lnc}.
#' @author Hajk-Georg Drost
#' @export
lnc_map_counts <- function(lnc_map, species_order) {
species <- NULL
all_lncRNAs_df <- dplyr::summarize(dplyr::group_by(lnc_map, species), n_orthologs = dplyr::n())
names(all_lncRNAs_df)[1] <- "subject_species"
all_lncRNAs_df$subject_species <- factor(
all_lncRNAs_df$subject_species,
levels = species_order
)
return(all_lncRNAs_df)
}