Nothing
#' @export
setGeneric("getProbeStats",
function(object) standardGeneric("getProbeStats"),
signature=c("object"))
#' @export
setGeneric("getProbesetIds",
function(object) standardGeneric("getProbesetIds"),
signature=c("object"))
#' @export
setGeneric("getNormalRegions",
function(object) standardGeneric("getNormalRegions"),
signature=c("object"))
#' @export
setGeneric("getNormalTissueRegions",
function(object) standardGeneric("getNormalTissueRegions"),
signature=c("object"))
#' Create an anti-profile from a AntiProfileStats object
#'
#' This function creates anti-profile using statistics stored in a AntiProfileStats object
#'
#' @param stats an object of class AntiProfileStats as produced by the apStats function
#' @param tissueSpec use tissue-specific regions of normal expression
#' @param tissueFilter use only tissue-specific genes in the anti-profile
#' @param sigsize desired size of signature, if NULL, computed from statCutoff
#' @param cutoff median absolute deviation multiplier used to define normal regions of expression
#' @param statCutoff cutoff used to include probesets in anti-profile
#' @return an object of class AntiProfilesSig or AntiProfilesTissueSig depending on the tissueSpec argument
#'
#' @examples
#' if (require(antiProfilesData)) {
#' # create an anti-profile, ignoring tissue-specificity of probesets, with 10 probesets
#' data(apColonData)
#' colonStats = apStats(exprs(apColonData), pData(apColonData)$Status)
#' ap = buildAntiProfile(colonStats, tissueSpec=FALSE, sigsize=10)
#' }
#'
#' @author Hector Corrada Bravo \email{hcorrada@@gmail.com}
#'
#' @export
#' @docType methods
#' @rdname buildAntiProfile-methods
setGeneric("buildAntiProfile",
function(stats, tissueSpec=TRUE, ...) standardGeneric("buildAntiProfile"),
signature=c("stats"))
#' Obtain the anti-profile score for a set of samples
#'
#' This function applies the given anti-profile to a new set of samples. Rownames in the expression matrix
#' are used to match probenames in the AntiProfile object.
#'
#' @param fit an object of class AntiProfile as produced by the buildAntiProfile method
#' @param expr a matrix of gene expression, rownames are used as identifiers
#' @return a numeric vector of anti-profile scores
#'
#' @examples
#' if (require(antiProfilesData)) {
#' data(apColonData)
#'
#' # compute statistics
#' colonStats = apStats(exprs(apColonData), pData(apColonData)$Status)
#'
#' # create an anti-profile, ignoring tissue-specificity of probesets, with 10 probesets
#' ap = buildAntiProfile(colonStats, tissueSpec=FALSE, sigsize=10)
#'
#' # get counts for the original dataset
#' counts =apCount(ap, exprs(apColonData))
#' }
#'
#' @author Hector Corrada Bravo \email{hcorrada@@gmail.com}
#'
#' @export
#' @docType methods
#' @rdname apCount-methods
setGeneric("apCount",
function(fit, expr, ...) standardGeneric("apCount"),
signature=c("fit", "expr"))
#' Reorder an AntiProfileStats object
#'
#' Reorders given AntiProfileStats object using provided ordering o
#'
#'
#' @param stats An object of class AntiProfileStats
#' @param o A numeric vector giving new probe ordering
#' @return A reordered AntiProfileStats object
#'
#' @examples
#' if (require(antiProfilesData)) {
#' data(apColonData)
#' colonStats = apStats(exprs(apColonData), pData(apColonData)$Status)
#' o = sample(seq(len=nrow(slot(colonStats,"probes"))))
#' newStats = apReorder(colonStats, o)
#' }
#'
#' @author Hector Corrada Bravo \email{hcorrada@@gmail.com}
#'
#' @export
#' @docType methods
#' @rdname apReorder-methods
setGeneric("apReorder",
function(stats, o) standardGeneric("apReorder"),
signature=c("stats","o"))
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.