get_deg_all function

get_deg_all

do diffiencial analysis according to exprission set and group information

get_deg_all(
  exp,
  group_list,
  ids,
  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 = FALSE,
  entriz = TRUE,
  n_cutoff = 2,
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

Arguments

• exp: A numeric matrix
• group_list: A factor with duplicated character or factor
• ids: a data.frame with 2 columns,including probe_id and symbol
• symmetry: a logical value ,would you like to get your plot symmetrical
• my_genes: genes for pheatmap
• show_rownames: logical,show rownames or not
• cluster_cols: boolean values determining if columns should be clustered or hclust object.
• color_volcano: color for volcano
• logFC_cutoff: Cutoff value of logFC,1 by default.
• pvalue_cutoff: Cutoff value of pvalue,0.05 by default.
• adjust: a logical value, would you like to use adjusted pvalue to draw this plot,FAlSE by default.
• entriz: logical , if TRUE ,convert symbol to entriz id.
• n_cutoff: 3 by defalut , scale before plot and set a cutoff,usually 2 or 1.6
• annotation_legend: logical,show annotation legend or not
• lab: label for x axis in volcano plot, if NA , x axis names by package
• species: choose human or mouse, or rat, default: human

Returns

a list with deg data.frame, volcano plot ,pca plot ,heatmap and a list with DEGs.

Examples

## Not run:

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)
  }
}
## End(Not run)

See Also

get_deg;multi_deg_all

Author(s)

Xiaojie Sun