R/commonArguments.R

In PavlidisLab/ermineR: Gene set analysis with multifunctionality assessment

#' scores
#' 
#' @keywords internal ORA GSR ROC
#' 
#' @name scores
#' 
#' @param scores A data.frame. Rownames have to be gene identifiers (eg. probes,
#'   must be unique), followed by any number of columns. The column used for
#'   scoring is chosen by \code{scoreColumn}. See
#'   \url{http://erminej.msl.ubc.ca/help/input-files/gene-scores/} for
#'   information abot how to specify scores. (for test = ORA, GSR and ROC)
#' @param scoreColumn Integer or character. Which column of the \code{scores} data.frame
#' to use as scores. Defaults to first column of \code{scores}. See
#' \url{http://erminej.msl.ubc.ca/help/input-files/gene-scores/} for details.
#' (for test = ORA, GSR and ROC)
#' @param bigIsBetter Logical. If TRUE large scores are considered to be higher.
#' \code{FALSE} by default (as in p values).
#' @param logTrans Logical. Should the data be -log10 transformed. Recommended for 
#' p values. \code{FALSE} by default
#' 
scores = function(scores,
                  scoreColumn = 1,
                  bigIsBetter = FALSE,
                  logTrans = FALSE){}

#' hitlist
#' 
#' @keywords internal ORA
#' 
#' @name hitlist
#' 
#' @param hitlist A vector of gene identifiers. ORA method accepts hitlists
#' instead of scores. If a hitlist is provided, logTrans, thresholds and 
#' bigIsBetter options are ignored.
hitlist = function(hitlist = NULL){
    
}

#' annotation
#' 
#' @keywords internal universal
#' 
#' @name annotation
#' 
#' @param annotation Annotation. A file path, a data.frame or a platform short 
#' name (eg. GPL127). If given a platform short name it will be downloaded
#' from annotation repository of Pavlidis Lab (\url{https://gemma.msl.ubc.ca/annots/}). 
#' To get a list of available annotations, use \code{\link{listGemmaAnnotations}}.
#' Note that if there is a file or folder with the same name as the platform 
#' name in the directory, that file will be read instead of getting a copy from 
#' Pavlidis Lab. If this file isn't a valid annotation file, the function will fail.
#' If providing a custom annotation file, see \code{\link{makeAnnotation}} to do it from
#' R or  \url{erminej.msl.ubc.ca/help/input-files/gene-annotations/} to do it manually.
#' 
#' If you are providing a custom gene set, you can leave annotation as NULL
#' @param aspects Character vector. Which Go aspects to include in the analysis.
#' Can be in long form (eg. 'Molecular Function') or short form (eg. \code{c('M','C','B')})
#' 
annotation = function(annotation,
                      aspects = c('Molecular Function','Cellular Component', 'Biological Process')){}


#' threshold
#' 
#' @keywords internal ORA
#' 
#' @name threshold
#' 
#' @param threshold Double. Score threshold (test = ORA only)
#'
threshold = function(threshold = 0.001){}



#' GSRstats
#' 
#' @keywords internal GSR
#' 
#' @name GSRstats
#' 
#' @param stats Method for computing raw class statistics (test = GSR only)
#' @param quantile Integer. Quantile to use. (stats = meanAboveQuantile only)
GSRstats = function(stats =  c('mean','quantile','meanAboveQuantile','precisionRecall'),
                    quantile = 50){}

#' expression
#' 
#' @keywords internal CORR
#' 
#' @name expression
#' 
#' @param expression A file path or a data frame. Expression data. (test = CORR only)
#' Necesary correlation anaylsis. See http://erminej.msl.ubc.ca/help/input-files/gene-expression-profiles/
#' for data format
#' 
expression = function(expression){}

#' iterations
#' 
#' @keywords internal GSR CORR precRecall
#' 
#' @name iterations
#' 
#' @param iterations Number of iterations. We suggest a starting value of 10000 
#' iterations. When you decide on parameters you like, we recommend a larger
#' number of iterations (perhaps 200,000 or more). This is to get sufficient
#' precision in the p-values to make multiple-test correction work correctly. 
#' (test = GSR CORR and precRecall methods only)
#' 
iterations = function(iterations = 10000){}

#' generalStats
#' 
#' @keywords internal universal
#' 
#' @name generalStats
#' 
#' @param geneReplicates  What to do when genes have multiple scores in input file
#'  (due to multiple probes per gene)
#' @param pAdjust Which multiple test correction method to use. Can be "FDR" or
#' 'Westfall-Young' (slower).
#' 
generalStats = function(geneReplicates = c('mean','best'),
                        pAdjust = c('FDR','Bonferroni')){}


#' geneSetOpts
#' 
#' @keywords internal universal
#' 
#' @name geneSetOpts
#' 
#' @param geneSetDescription "Latest_GO", a file path that leads to a GO XML or OBO file
#' or a URL that leads to a go ontology file that ends with rdf-xml.gz. 
#' 
#' If you left annotation as NULL and provided customGeneSets, this argument is
#' not required and will default to NULL. Otherwise, by default it'll be set to
#' "Latest_GO" which downloads the latest available GO XML file. This option won't work
#' without an internet connection. To get a frozen file
#' that you can use later, see \code{\link{goToday}}, \code{\link{goAtDate}} and \code{\link{getGoDates}}.
#'  See \url{http://erminej.msl.ubc.ca/help/input-files/gene-set-descriptions/}
#' for details.
#' 
#' 
#' @param customGeneSets Path to a directory that contains custom gene set files,
#'  paths to custom gene set files themselves or a named list of character strings.
#' Use this option to create your own gene sets. If you provide directory you can
#' specify probes or gene symbols to include in your gene sets. 
#' See \url{http://erminej.msl.ubc.ca/help/input-files/gene-sets/}
#' for information about format for this file. If you are providing a list, only gene
#' symbols are accepted.
#' @param minClassSize minimum class size
#' @param maxClassSize maximum class size
geneSetOpts = function(geneSetDescription = 'Latest_GO',
                       customGeneSets = NULL,
                       minClassSize = 20,
                       maxClassSize = 200){}

#' returnOptions
#' 
#' @keywords internal universal
#' 
#' @name returnOpts
#' 
#' @param output Output file name. 
#' @param return If results should be returned. Set to FALSE if you only want a file
#' 
returnOptions = function(output = NULL,
                         return = TRUE){}