使用方法:

$Rscript $scriptdir/edger_analysis.r -h
usage: /work/my_stad_immu/scripts/edger_analysis.r [-h] -i 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]

edgeR analysis : https://www.omicsclass.com/article/1506

optional arguments:
  -h, --help            show this help message and exit
  -i filepath, --input filepath
                        input read count file [required]
  -m filepath, --metadata filepath
                        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
                        /work/my_stad_immu/05.enrich]
  -p prefix, --prefix prefix
                        out file name prefix [default Volcano]

参数说明：

-i 输入基因表达矩阵文件，必须为count表达文件：

-m metadata文件路径,样本的分组信息，第一列必须和表达文件的样本名称对应：

-t subtype.hclust   --case S1 --control  S2  ： 指定metadata 分组列名，分组里面的比较组名字 ，如果分组名字有空格，应该用引号引起来：  “Stage IA”

--fdr 0.01 --fc 2  设置差异基因的筛选条件： 显著性和差异倍数

使用举例：

Rscript $scriptdir/edger_analysis.r  -i ../01.TCGA_download/TCGA-STAD_gene_expression_Counts.tsv \
    --fdr 0.01 --fc 2 \
  -m ../03.TIME/metadata.group.tsv -t subtype.hclust   --case S1 --control  S2 -p S1_vs_S2

结果展示：

火山图：

脚本获取与使用课程：https://study.163.com/course/introduction/1211864801.htm?share=1&shareId=1030291076

参考文献：

Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.

McCarthy DJ, Chen Y, Smyth GK (2012). “Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.” Nucleic Acids Research, 40(10), 4288-4297. doi: 10.1093/nar/gks042.