@@ -12,7 +12,8 @@

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

 #' @examples

 #' 

-#' # see vignette

+#' dataDirectory <- system.file("extdata", package="metagenomeSeq")

+#' clin = loadPhenoData(file.path(dataDirectory,"CHK_clinical.csv"),tran=TRUE)

 #' 

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

 {

new file mode 100644

@@ -0,0 +1,51 @@

+#' 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

+#' 

+#' # see vignette

+#' 

+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);

+}