#' Load a clinical/phenotypic dataset associated with a study.

 #' 

 #' Load a matrix of metadata associated with a study.

 #' 
 #' 

 #' @aliases loadPhenoData phenoData

 #' @param file Path and filename of the actual clinical file.

 #' @param tran Boolean. If the covariates are along the columns and samples
 #' along the rows, then tran should equal TRUE.

 #' @param sep The separator for the file.
 #' @return The metadata as a dataframe.

 #' @seealso \code{\link{loadMeta}}

 #' @examples

 #' 

 #' dataDirectory <- system.file("extdata", package="metagenomeSeq")
 #' clin = loadPhenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)

 #' 

 loadPhenoData <-function(file,tran=TRUE,sep="\t")

 {
 	dat2 <- read.table(file,header=FALSE,sep=sep);
 
 # no. of subjects 
 	subjects <- array(0,dim=c(ncol(dat2)-1));
 	for(i in 1:length(subjects)) {
 		subjects[i] <- as.character(dat2[1,i+1]);
 	}
 # no. of rows
 	rows <- nrow(dat2);
 	
 # load remaining counts
 	matrix <- array(NA, dim=c(length(subjects),rows-1));
 	covar = array(NA,dim=c(rows-1,1)); 
 	
 	for(i in 1:(rows)-1){
 		for(j in 1:(length(subjects))){ 
 			matrix[j,i] <- as.character(dat2[i+1,j+1]);
 		}
 		covar[i] = as.character(dat2[i+1,1]);
 	}  
 	
 		
 	phenoData<-as.data.frame(matrix);
 	
 	colnames(phenoData) = covar;
 	if(length(unique(subjects))==(length(subjects))){
 		rownames(phenoData) = subjects;
 	}
     if(tran==TRUE){
         phenoData = as.data.frame(t(phenoData))
 	}
 	return(phenoData);
 }