% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/DE_functions.R
 \name{DEGs_RP}
 \alias{DEGs_RP}
 \title{return DEGs UP and DOWN list based on Rank Product}
 \usage{
 DEGs_RP(
   tfit,

   lfc = NULL,

   p = 0.05,
   assemble = "intersect",
   Rank = "adj.P.Val",
   nperm = 1e+05,

   thres = 0.05,

   keep.top = NULL,
   keep.group = NULL,
   ...
 )
 }
 \arguments{
 \item{tfit}{MArrayLM object generated by \code{\link[limma:ebayes]{limma::treat()}}}
 
 \item{lfc}{num, cutoff of logFC for DE analysis}
 

 \item{p}{num, cutoff of p value for DE analysis}

 
 \item{assemble}{'intersect' or 'union', whether to select intersected or
 union genes of different comparisons, default 'intersect'}
 

 \item{Rank}{character, the variable for ranking DEGs, can be 'logFC',
 'adj.P.Val'..., default 'adj.P.Val'}

 
 \item{nperm}{num, permutation runs of simulating the distribution}
 

 \item{thres}{num, cutoff for rank product permutation test if
 feature_selection = "rankproduct", default 0.05}

 \item{keep.top}{NULL or num, whether to keep top n DEGs of specific
 comparison}

 \item{keep.group}{NULL or pattern, specify the top DEGs of which comparison

 or group to be kept}

 
 \item{...}{omitted}

 }

 \value{
 A list of "UP" and "DOWN" genes
 }

 \description{
 return DEGs UP and DOWN list based on Rank Product
 }