man/patternMarkers-methods.Rd
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 % Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R
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 \docType{methods}
 \name{patternMarkers}
 \alias{patternMarkers}
 \alias{patternMarkers,CogapsResult-method}
 \title{compute pattern markers statistic}
 \usage{
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 patternMarkers(object, threshold = "all", lp = NA)
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 \S4method{patternMarkers}{CogapsResult}(object, threshold = "all",
   lp = NA)
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 }
 \arguments{
 \item{object}{an object of type CogapsResult}
 
 \item{threshold}{the type of threshold to be used. The default "all" will
 distribute genes into pattern with the lowest ranking. The "cut" thresholds
 by the first gene to have a lower ranking, i.e. better fit to, a pattern.}
 
 \item{lp}{a vector of weights for each pattern to be used for finding
 markers. If NA markers for each pattern of the A matrix will be used.}
 }
 \value{
 By default a non-overlapping list of genes associated with each
 \code{lp}. If \code{full=TRUE} a data.frame of genes rankings with a column
 for each \code{lp} will also be returned.
 }
 \description{
 calculate the most associated pattern for each gene
 }