R/ebbc_load_critical_sigma.R

In LeonardoRicci/EBBC: Expression-Based Bayesian Classifier

## --------------------------------------------------------------------------
##
## This file is part of the EBBC software package.
##
## Version 1.0 - January 2020
##
##
## The EBBC package is free software; you can use it, redistribute it,
## and/or modify it under the terms of the GNU General Public License
## version 3 as published by the Free Software Foundation. The full text
## of the license can be found in the file LICENSE.txt at the top level of
## the package distribution.
##
## Authors:
##	Michele Castelluzzo (1), Alessio Perinelli (1),
##		Michela A. Denti (2) and Leonardo Ricci (1,3)
##	(1) Department of Physics, University of Trento, 38123 Trento, Italy
##	(2) Department of Cellular, Computational and Integrative Biology
##		(CIBIO), University of Trento, 38123 Trento, Italy
##	(3) CIMeC, Center for Mind/Brain Sciences, University of Trento,
##		38068 Rovereto, Italy
##
##	michele.castelluzzo@unitn.it
##	alessio.perinelli@unitn.it
##	michela.denti@unitn.it
##	leonardo.ricci@unitn.it
##	https://github.com/LeonardoRicci/
##	https://nse.physics.unitn.it/
##
##
## If you use the EBBC package for your analyses, please cite:
##
##	L. Ricci, V. Del Vescovo, C. Cantaloni, M. Grasso, M. Barbareschi and
##	M. A. Denti, Statistical analysis of a Bayesian classifier based on the
##	expression of miRNAs, BMC Bioinformatics 16:287 (2015).
##	DOI: 10.1186/s12859-015-0715-9
##
##
## --------------------------------------------------------------------------

#' Load critical sigma values.
#'
#' This function loads from file a data frame containing the critical sigma values for a set of features.
#'
#' @param inputFileName Name of the file to be loaded. The file has to contain at least the columns 'Feature', 'SigmaMax' (not necessarily in this order).
#' @param sep Field separator character; the default is any white space (one or more spaces or tabulations).
#'
#' @return A data frame containing the columns 'Feature' and 'SigmaMax'.

#' @export
ebbc_loadCriticalSigma <- function(inputFileName, sep="") {

	cat("\nLOG: ebbc_loadCriticalSigma() called.\n")

	if (!file.exists(inputFileName)) {
		cat("ERROR: cannot read ", inputFileName, ". No such file or directory.\n")
		return(NULL)
	} else if (file.access(inputFileName, mode=4)) {
		cat("ERROR: cannot read ", inputFileName, ". Check read permission.\n")
		return(NULL)
	}

	if (sep == "") {
		readFrame <- utils::read.table(file=inputFileName, fileEncoding="UTF-8", header=T)
	} else {
		readFrame <- utils::read.table(file=inputFileName, sep=sep, fileEncoding="UTF-8", header=T)
	}

	if (!(("Feature" %in% colnames(readFrame)) & ("SigmaMax" %in% colnames(readFrame)))) {
		cat("ERROR: unsuitable dataset format. Dataset must contain columns 'Feature', 'SigmaMax'.\n")
		return(NULL)
	}

	if (length(readFrame[1,]) > 2) {
		cat("WARNING: more than 2 dataset columns. Columns other than 'Feature', 'SigmaMax' will be ignored.\n")
	}

	outputFrame <- subset(readFrame, select=c("Feature", "SigmaMax"))

	cat("LOG:\tCritical sigma values loaded from ", inputFileName, " successfully.\n", sep="")

	return(outputFrame)
}