R/get.gene.summary.stats.R

In NanoStringNorm: Normalize NanoString miRNA and mRNA Data

# The NanoStringNorm package is copyright (c) 2012 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
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get.gene.summary.stats <- function(x, anno = NA) {

	gene.summary.stats <- apply(
		X = x,
		MARGIN = 1,
		FUN = get.mean.sd.and.cv
		);

	gene.summary.stats <- t(gene.summary.stats);

	# calculate count of missing values (DW missing could be moved to own function)
	genes.proportion.missing <- apply(
		X = x,
		MARGIN = 1,
		FUN = function(y) { sum(y <= 0, na.rm = TRUE) / length(y) }
		);

	gene.summary.stats <- cbind(gene.summary.stats, 100 * genes.proportion.missing);

	gene.summary.stats <- round(gene.summary.stats, 1);
	colnames(gene.summary.stats) <- c("Mean", "SD", "CV", "Missing");
	rownames(gene.summary.stats) <- anno$Name;

	return(gene.summary.stats);
	}