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Merge pull request #40 from HCBravoLab/deprecate

Creating naming schemes consistency and deprecating the load_* functions.

From: Joseph N. Paulson <jpaulson@jimmy.harvard.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq@121795 bc3139a8-67e5-0310-9ffc-ced21a209358

Hector Corrada Bravo authored on 05/10/2016 10:10:48
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+#' Load a count dataset associated with a study set up in a Qiime format.
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+#' 
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+#' Load a matrix of OTUs in Qiime's format
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+#' 
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+#' 
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+#' @aliases loadMetaQ qiimeLoader
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+#' @param file Path and filename of the actual data file.
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+#' @return An list with 'counts' containing the count data, 'taxa' containing the otu annotation, and 'otus'.
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+#' @seealso \code{\link{loadMeta}} \code{\link{loadPhenoData}}
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+#' @examples
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+#' 
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+#' # see vignette
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+#' 
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+loadMetaQ <- function(file) {	
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+	dat2 <- read.delim(file,header=FALSE,stringsAsFactors=FALSE,nrows=1,skip=1);
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+	len = ncol(dat2)
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+	subjects = as.character(dat2[1,-c(1,len)]);
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+	classes <-c("character",rep("numeric",(len-2)),"character");
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+	dat3 <- read.delim(file,header=TRUE,colClasses=classes,skip=1);
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+	taxa<- dat3[,len];
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+	taxa<-as.matrix(taxa);
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+	matrix <- dat3[,-c(1,len)]
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+	colnames(matrix) = subjects;
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+	otus = dat3[,1];
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+	rownames(matrix) = otus;
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+	obj <- list(counts=as.data.frame(matrix), taxa=as.data.frame(taxa),otus = as.data.frame(otus))
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+	return(obj);
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+}