文章目录
- $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.亿速云.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]
- -i 输入基因表达矩阵文件，必须为count表达文件： ID TCGA-B7-A5TK-01A-12R-A36D-31 TCGA-BR-7959-01A-11R-2343-13 TCGA-IN-8462-01A-11R-2343-13 TCGA-BR-A4CR-01A-11R-A24K-31 TCGA-CG-4443-01A-01R-1157-13 TCGA-KB-A93J-01A-11R-A39E-31 TCGA-BR-4371-01A-01R-1157-13 TSPAN6 5951 4036 2834 3484 2537 2027 4749 TNMD 3 4 0 1 0 1 8 DPM1 4672 4330 1725 4370 6523 3094 4415 SCYL3 1260 2057 702 1483 924 1451 982 C1orf112 523 992 172 1400 234 733 958 FGR 1249 1127 285 148 56 941 208 CFH 12831 11435 5387 995 4571 2189 1795 FUCA2 5896 7857 3208 5625 1527 7530 3290 GCLC 2682 5509 1447 9323 6422 5265 2418 -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： barcode subtype.hclust StromalScore ImmuneScore ESTIMATEScore TumourPurity TCGA-B7-A5TK-01A-12R-A36D-31 S1 1026.057 2386.835 3412.892 0.448276 TCGA-BR-7959-01A-11R-2343-13 S2 1130.722 729.402 1860.124 0.638667 TCGA-IN-8462-01A-11R-2343-13 S2 112.2318 683.9349 796.1667 0.750581 TCGA-BR-A4CR-01A-11R-A24K-31 S2 -1060.35 -766.618 -1826.97 0.943814 TCGA-CG-4443-01A-01R-1157-13 S2 -261.577 -258.629 -520.206 0.8635 TCGA-KB-A93J-01A-11R-A39E-31 S1 -202.255 1605.12 1402.865 0.688838 TCGA-BR-4371-01A-01R-1157-13 S2 -828.231 711.3379 -116.893 0.832147 TCGA-IN-A6RO-01A-12R-A33Y-31 S2 -1406.57 68.58307 -1337.98 0.917683 TCGA-HU-A4H3-01A-21R-A251-31 S2 -619.208 538.7225 -80.4854 0.829171 TCGA-RD-A8MV-01A-11R-A36D-31 S1 113.4127 2309.647 2423.06 0.572976 TCGA-VQ-A91X-01A-12R-A414-31 S2 -1845.85 -590.017 -2435.87 0.969545 TCGA-D7-8575-01A-11R-2343-13 S2 -206.112 1392.799 1186.687 0.711491 TCGA-BR-4257-01A-01R-1131-13 S1 861.029 1676.148 2537.177 0.559167 TCGA-BR-8485-01A-11R-2402-13 S1 373.0961 1110.516 1483.612 0.680198 TCGA-BR-4370-01A-01R-1157-13 S1 1300.495 1802.327 3102.822 0.488483 -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
- 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
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edger_analysis.r 差异基因分析edgeR
$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.亿速云.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]
-i 输入基因表达矩阵文件，必须为count表达文件：
| ID | TCGA-B7-A5TK-01A-12R-A36D-31 | TCGA-BR-7959-01A-11R-2343-13 | TCGA-IN-8462-01A-11R-2343-13 | TCGA-BR-A4CR-01A-11R-A24K-31 | TCGA-CG-4443-01A-01R-1157-13 | TCGA-KB-A93J-01A-11R-A39E-31 | TCGA-BR-4371-01A-01R-1157-13 |
| TSPAN6 | 5951 | 4036 | 2834 | 3484 | 2537 | 2027 | 4749 |
| TNMD | 3 | 4 | 0 | 1 | 0 | 1 | 8 |
| DPM1 | 4672 | 4330 | 1725 | 4370 | 6523 | 3094 | 4415 |
| SCYL3 | 1260 | 2057 | 702 | 1483 | 924 | 1451 | 982 |
| C1orf112 | 523 | 992 | 172 | 1400 | 234 | 733 | 958 |
| FGR | 1249 | 1127 | 285 | 148 | 56 | 941 | 208 |
| CFH | 12831 | 11435 | 5387 | 995 | 4571 | 2189 | 1795 |
| FUCA2 | 5896 | 7857 | 3208 | 5625 | 1527 | 7530 | 3290 |
| GCLC | 2682 | 5509 | 1447 | 9323 | 6422 | 5265 | 2418 |
-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：
| barcode | subtype.hclust | StromalScore | ImmuneScore | ESTIMATEScore | TumourPurity |
| TCGA-B7-A5TK-01A-12R-A36D-31 | S1 | 1026.057 | 2386.835 | 3412.892 | 0.448276 |
| TCGA-BR-7959-01A-11R-2343-13 | S2 | 1130.722 | 729.402 | 1860.124 | 0.638667 |
| TCGA-IN-8462-01A-11R-2343-13 | S2 | 112.2318 | 683.9349 | 796.1667 | 0.750581 |
| TCGA-BR-A4CR-01A-11R-A24K-31 | S2 | -1060.35 | -766.618 | -1826.97 | 0.943814 |
| TCGA-CG-4443-01A-01R-1157-13 | S2 | -261.577 | -258.629 | -520.206 | 0.8635 |
| TCGA-KB-A93J-01A-11R-A39E-31 | S1 | -202.255 | 1605.12 | 1402.865 | 0.688838 |
| TCGA-BR-4371-01A-01R-1157-13 | S2 | -828.231 | 711.3379 | -116.893 | 0.832147 |
| TCGA-IN-A6RO-01A-12R-A33Y-31 | S2 | -1406.57 | 68.58307 | -1337.98 | 0.917683 |
| TCGA-HU-A4H3-01A-21R-A251-31 | S2 | -619.208 | 538.7225 | -80.4854 | 0.829171 |
| TCGA-RD-A8MV-01A-11R-A36D-31 | S1 | 113.4127 | 2309.647 | 2423.06 | 0.572976 |
| TCGA-VQ-A91X-01A-12R-A414-31 | S2 | -1845.85 | -590.017 | -2435.87 | 0.969545 |
| TCGA-D7-8575-01A-11R-2343-13 | S2 | -206.112 | 1392.799 | 1186.687 | 0.711491 |
| TCGA-BR-4257-01A-01R-1131-13 | S1 | 861.029 | 1676.148 | 2537.177 | 0.559167 |
| TCGA-BR-8485-01A-11R-2402-13 | S1 | 373.0961 | 1110.516 | 1483.612 | 0.680198 |
| TCGA-BR-4370-01A-01R-1157-13 | S1 | 1300.495 | 1802.327 | 3102.822 | 0.488483 |
-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
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