R/annotations_all.R

In act: Aligned Corpus Toolkit

#' All annotations in a corpus
#'
#' Merges annotations from all transcripts in a corpus and returns a data frame.
#' 
#' @param x Corpus object.
#'
#' @return Data.frame.
#' @export
#'
#' @examples
#' 
#' library(act)
#' 
#' #Get data frame with all annotations
#' allannotations <- act::annotations_all(examplecorpus)
#' 
#' #Have a look at the number of annotations
#' nrow(allannotations)
#' 
annotations_all <- function(x) {
	if (missing(x)) 	{stop("Corpus object in parameter 'x' is missing.") 		}	else { if (!methods::is(x,"corpus")   )	{stop("Parameter 'x' needs to be a corpus object.") } }
	temp <- data.frame()
	temp <- NULL
	for (t in x@transcripts) {
		if (is.null(temp)) {
			if (nrow(t@annotations)>0) {
				temp <- cbind(transcript.name=rep(t@name, nrow(t@annotations)),  t@annotations)	
			}
		} else {
			if (nrow(t@annotations)>0) {
				temp <- rbind(temp, cbind(transcript.name=rep(t@name, nrow(t@annotations)),  t@annotations))	
			}
		}
	}
	return(temp)
}