edger_analysis.r 差异基因分析edgeR

edger_analysis.r 差异基因分析edgeR

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:

IDTCGA-B7-A5TK-01A-12R-A36D-31TCGA-BR-7959-01A-11R-2343-13TCGA-IN-8462-01A-11R-2343-13TCGA-BR-A4CR-01A-11R-A24K-31TCGA-CG-4443-01A-01R-1157-13TCGA-KB-A93J-01A-11R-A39E-31TCGA-BR-4371-01A-01R-1157-13
TSPAN65951403628343484253720274749
TNMD3401018
DPM14672433017254370652330944415
SCYL31260205770214839241451982
C1orf1125239921721400234733958
FGR1249112728514856941208
CFH12831114355387995457121891795
FUCA25896785732085625152775303290
GCLC2682550914479323642252652418


-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:


barcodesubtype.hclustStromalScoreImmuneScoreESTIMATEScoreTumourPurity
TCGA-B7-A5TK-01A-12R-A36D-31S11026.0572386.8353412.8920.448276
TCGA-BR-7959-01A-11R-2343-13S21130.722729.4021860.1240.638667
TCGA-IN-8462-01A-11R-2343-13S2112.2318683.9349796.16670.750581
TCGA-BR-A4CR-01A-11R-A24K-31S2-1060.35-766.618-1826.970.943814
TCGA-CG-4443-01A-01R-1157-13S2-261.577-258.629-520.2060.8635
TCGA-KB-A93J-01A-11R-A39E-31S1-202.2551605.121402.8650.688838
TCGA-BR-4371-01A-01R-1157-13S2-828.231711.3379-116.8930.832147
TCGA-IN-A6RO-01A-12R-A33Y-31S2-1406.5768.58307-1337.980.917683
TCGA-HU-A4H3-01A-21R-A251-31S2-619.208538.7225-80.48540.829171
TCGA-RD-A8MV-01A-11R-A36D-31S1113.41272309.6472423.060.572976
TCGA-VQ-A91X-01A-12R-A414-31S2-1845.85-590.017-2435.870.969545
TCGA-D7-8575-01A-11R-2343-13S2-206.1121392.7991186.6870.711491
TCGA-BR-4257-01A-01R-1131-13S1861.0291676.1482537.1770.559167
TCGA-BR-8485-01A-11R-2402-13S1373.09611110.5161483.6120.680198
TCGA-BR-4370-01A-01R-1157-13S11300.4951802.3273102.8220.488483


-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:



attachments-2021-06-vixQomQb60d2b01a431c0.png


参考文献:

Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics26(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 Research40(10), 4288-4297. doi: 10.1093/nar/gks042.

  • 发表于 2021-06-25 11:21
  • 阅读 ( 77 )
  • 分类:转录组

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