How to use univariate_cox.r in R language
This article mainly introduces the R language univariate_cox.r how to use the relevant knowledge, the content is detailed and easy to understand, the operation is simple and fast, has a certain reference value, I believe you will gain something after reading this article on how to use univariate_cox.r in R language, let's take a look.
Univariate cox regression analysis
How to use it:
Specify a single variable for cox regression analysis, which can be clinical data
$Rscript $scriptdir/univariate_cox.r-husage: / 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 regressionoptional 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] example: 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 parameter description:
-I input survival data and clinical data
BarcodeTIMEEVENTFGRCD38ITGALCX3CL1CEACAM21MATKCD79BMMP25TCGA-B7-A5TK-01A-12R-A36D-31288016.3440886.8677240.26903603.01321.8685362.283423.45319813.72829TCGA-BR-7959-01A-11R-2343-131010011.9673915.794517.35856626.913532.5719170.8641161.8799573.451148TCGA-IN-8462-01A-11R-2343-1357205.3508463.1113423.76912520.222380.6108390.5197762.8221921.106563TCGA-CG-4443-01A-01R-1157-1391201.538020.8629552.3735119.040971.0921270.7603481.9265920.878735TCGAMube A93JMuir 01A- 11R-A39E-311124015.2401613.304738.0859114.152953.4835593.1929513.65174210.43186TCGA-HU-A4H3-01A-21R-A251-3188206.2617612.6751737.0258864.0502710.5841591.0393361.9792142.312993TCGA-RD-A8MV-01A-11R-A36D-313720027.0741520.1588534.9130934.718214.1131122.61555716.5194617.72674TCGA-VQ-A91X-01A-12R-A414-3128911.0623410.7520182.3805134.4158150.5181420.2121971.2392030.582114
Result display: VariableTermBetaHRHRlowerHRupperPriskScoreriskScore1.3124753.7153562.3299775.9244683.53E-08ajcc_pathologic_stageajcc_pathologic_stageStage IV1.4190894.1333531.9438288.7891540.000227ajcc_pathologic_stageajcc_pathologic_stageStage III0.8551992.3518431.2037484.5949530.012327age_at_indexage_at_index0.0181241.0182891.0007321.0361540.04111ajcc_pathologic_stageajcc_pathologic_stageStage II0.5336181.705090.8381573.4687170.140829gendergendermale0.2178161.2433580.8579621.8018740.249868
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