% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/5_get_deg_all.R
\name{get_deg_all}
\alias{get_deg_all}
\title{get_deg_all}
\usage{
get_deg_all(
  exp,
  group_list,
  ids = NULL,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = TRUE,
  entriz = TRUE,
  n_cutoff = 2,
  annotation_legend = FALSE,
  lab = NA,
  change_col = "change",
  species = "human"
)
}
\arguments{
\item{exp}{A numeric matrix}

\item{group_list}{A character or factor vector with one label per sample;
character input will be converted to factor and unused levels will be
dropped.}

\item{ids}{optional probe-to-symbol annotation table. If `NULL`, `exp` is
treated as a gene-level matrix and no ID conversion is performed.}

\item{symmetry}{a logical value ,would you like to get your plot symmetrical}

\item{my_genes}{genes for pheatmap}

\item{show_rownames}{logical,show rownames or not}

\item{cluster_cols}{boolean values determining if columns should be clustered or \code{hclust} object.}

\item{color_volcano}{color for volcano}

\item{logFC_cutoff}{Cutoff value of logFC,1 by default.}

\item{pvalue_cutoff}{Cutoff value of pvalue,0.05 by default.}

\item{adjust}{a logical value; if TRUE, use \code{padj} and plot
\code{-log10(padj)}; otherwise use \code{P.value} and plot
\code{-log10(P.value)}.}

\item{entriz}{logical, if TRUE, convert symbols to Entrez IDs.}

\item{n_cutoff}{numeric cutoff used after scaling; values outside
\code{[-n_cutoff, n_cutoff]} are truncated before plotting.}

\item{annotation_legend}{logical,show annotation legend or not}

\item{lab}{label for  x axis in volcano plot; when `NA`, pkg = 4 uses
`log2FoldChange`, and the other package codes keep their original labels}

\item{change_col}{column name for the up/down/status label. Default uses
`change` when it exists; otherwise the function falls back to the
existing automatic classification logic.}

\item{species}{choose human, mouse, or rat; default is human}
}
\value{
a list with a deg data.frame, volcano plot, PCA plot, heatmap, and
  a list with DEGs.
}
\description{
Do differential analysis according to an expression set and group
information.
}
\examples{
\dontrun{
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE42872"
  geo = geo_download(gse,destdir=tempdir())
  group_list = rep(c("A","B"),each = 3)
  group_list = factor(group_list)
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  dcp = get_deg_all(geo$exp,group_list,ids,entriz = FALSE)
  head(dcp$deg)
  dcp$plots
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}
}
}
\seealso{
\code{\link{get_deg}};\code{\link{multi_deg_all}}
}
\author{
Xiaojie Sun
}
