使用方法:

$Rscript DEG_limma.R -h
usage: DEG_limma.R [-h] -e filepath -m filepath -t treatname --control CONTROL
                   --case CASE [-f fdr] [-c fc] [-s size] [-a alpha]
                   [-X x.lab] [-Y y.lab] [-T title] [-H height] [-W width]
                   [-o path] [-p prefix]

limma analysis: https://www.omicsclass.com/article/1519

optional arguments:
  -h, --help            show this help message and exit
  -e filepath, --expr filepath
                        input read count file[required]
  -m filepath, --metadata filepath
                        input metadata file[required]
  -t treatname, --treatname treatname
                        treat colname in group file[required]
  --control CONTROL     set control group name[required]
  --case CASE           set case group name[required]
  -f fdr, --fdr fdr     set fdr threshold[default 0.05]
  -c fc, --fc fc        set fold change threshold[default 2]
  -s size, --size size  point size[optional,default:0.7]
  -a alpha, --alpha alpha
                        point transparency[0-1][optional,default:1]
  -X x.lab, --x.lab x.lab
                        the label for x axis[optional,default:log2FC]
  -Y y.lab, --y.lab y.lab
                        the label for y axis[optional,default:-log10(FDR)]
  -T title, --title title
                        the label for main title[optional,default:Volcano]
  -H height, --height height
                        the height of pic inches[default:5]
  -W width, --width width
                        the width of pic inches[default:5]
  -o path, --outdir path
                        output file directory[default:/share/work/fangs]
  -p prefix, --prefix prefix
                        out file name prefix[default:Volcano]

$$Rscript DEG_limma.R -e TCGA-ESCA_gene_expression_Counts.tsv \
> --fdr 0.05 --fc 2 -m metadata.group.tsv -t subtype.hclust \
> --case S1 --control S2 -p S1_vs_S2.limma