man/patternMarkers-methods.Rd
 28e23637  % Generated by roxygen2: do not edit by hand  c045c620  % Please edit documentation in R/class-CogapsResult.R, R/methods-CogapsResult.R  28e23637  \docType{methods} \name{patternMarkers} \alias{patternMarkers} \alias{patternMarkers,CogapsResult-method} \title{compute pattern markers statistic} \usage{  c5bcadbc  patternMarkers(object, threshold = "all", lp = NA)  28e23637   c5bcadbc  \S4method{patternMarkers}{CogapsResult}(object, threshold = "all", lp = NA)  28e23637  } \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 }