使用方法：
指定单个变量做cox回归分析，可以是临床数据
$Rscript $scriptdir/univariate_cox.r -h
usage: /share/nas1/huangls/test/TCGA_immu/scripts/univariate_cox.r
[-h] -i data -t time -e event -v variate [variate ...] [-b blocksize]
[-o outdir] [-p prefix]
unvariate cox regression
optional arguments:
-h, --help show this help message and exit
-i data, --data data input data file path[required]
-t time, --time time set suvival time column name [required]
-e event, --event event
set event column name must 0 or 1 code format
[required]
-v variate [variate ...], --variate variate [variate ...]
variate for cox analysis [required]
-b blocksize, --blocksize blocksize
Number of variables Parallel to test in each [default
2]
-o outdir, --outdir outdir
output file directory [default cwd]
-p prefix, --prefix prefix
out file name prefix [default cox]
使用举例：
Rscript $scriptdir/univariate_cox.r -i nomogram_metadata.tsv -e EVENT -t TIME \
-v gender riskScore age_at_index ajcc_pathologic_stage \
-o univariate_cox \
-p univariate_cox
参数说明：
-i 输入生存数据与临床数据
| barcode | TIME | EVENT | FGR | CD38 | ITGAL | CX3CL1 | CEACAM21 | MATK | CD79B | MMP25 |
| TCGA-B7-A5TK-01A-12R-A36D-31 | 288 | 0 | 16.34408 | 86.86772 | 40.26903 | 603.0132 | 1.868536 | 2.28342 | 3.453198 | 13.72829 |
| TCGA-BR-7959-01A-11R-2343-13 | 1010 | 0 | 11.96739 | 15.79451 | 7.358566 | 26.91353 | 2.571917 | 0.864116 | 1.879957 | 3.451148 |
| TCGA-IN-8462-01A-11R-2343-13 | 572 | 0 | 5.350846 | 3.111342 | 3.769125 | 20.22238 | 0.610839 | 0.519776 | 2.822192 | 1.106563 |
| TCGA-CG-4443-01A-01R-1157-13 | 912 | 0 | 1.53802 | 0.862955 | 2.37351 | 19.04097 | 1.092127 | 0.760348 | 1.926592 | 0.878735 |
| TCGA-KB-A93J-01A-11R-A39E-31 | 1124 | 0 | 15.24016 | 13.3047 | 38.08591 | 14.15295 | 3.483559 | 3.192951 | 3.651742 | 10.43186 |
| TCGA-HU-A4H3-01A-21R-A251-31 | 882 | 0 | 6.261761 | 2.675173 | 7.025886 | 4.050271 | 0.584159 | 1.039336 | 1.979214 | 2.312993 |
| TCGA-RD-A8MV-01A-11R-A36D-31 | 3720 | 0 | 27.07415 | 20.15885 | 34.91309 | 34.71821 | 4.113112 | 2.615557 | 16.51946 | 17.72674 |
| TCGA-VQ-A91X-01A-12R-A414-31 | 289 | 1 | 1.062341 | 0.752018 | 2.380513 | 4.415815 | 0.518142 | 0.212197 | 1.239203 | 0.582114 |
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结果展示：
| Variable |
Term |
Beta |
HR |
HRlower |
HRupper |
P |
| riskScore |
riskScore |
1.312475 |
3.715356 |
2.329977 |
5.924468 |
3.53E-08 |
| ajcc_pathologic_stage |
ajcc_pathologic_stageStage IV |
1.419089 |
4.133353 |
1.943828 |
8.789154 |
0.000227 |
| ajcc_pathologic_stage |
ajcc_pathologic_stageStage III |
0.855199 |
2.351843 |
1.203748 |
4.594953 |
0.012327 |
| age_at_index |
age_at_index |
0.018124 |
1.018289 |
1.000732 |
1.036154 |
0.04111 |
| ajcc_pathologic_stage |
ajcc_pathologic_stageStage II |
0.533618 |
1.70509 |
0.838157 |
3.468717 |
0.140829 |
| gender |
gendermale |
0.217816 |
1.243358 |
0.857962 |
1.801874 |
0.249868 |
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R包 survival 完成分析
脚本获取与使用课程：https://study.163.com/course/introduction/1211864801.htm?share=1&shareId=1030291076
