How to use univariate_cox_batch.r in R language

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Batch single factor cox regression analysis of univariate_cox_batch.r gene expression

Instructions for use:

Input survival data and gene expression can be used for batch single factor cox regression analysis.

$Rscript $scriptdir/univariate_cox_batch.r-- husage: univariate_cox_batch.r [- h]-m metadata-g expset [- t time] [- e event] [- l pvalue] [- b blocksize] [--log2] [- o outdir] [- P prefix] batch unvariate cox regression gene expressionoptional arguments:-h -- help show this help message and exit-m metadata,-- metadata metadata input metadata file path with suvival time [required]-g expset,-- expset expset input gene expression set file [required]-t time,-- time time set suvival time column name in metadata [default TIME]-e event -- event event set event column name in metadata [default EVENT]-- l pvalue,-- pvalue cutoff to choose sig gene [default 0.01]-b blocksize -- blocksize blocksize Number of variables Parallel to test in each [default 2]-- log2 whether do log2 transfrom for expression data [optional, default: False]-o outdir,-- outdir outdir output file directory [default cwd]-p prefix -- prefix prefix out file name prefix [default cox] parameter description:

-m enter survival data:

Event column: 0 indicates that the event did not occur, 1 indicates that the event occurred, and 0 indicates that alive,1 indicates death

BarcodeTIMEEVENTTCGA-B7-A5TK-01A-12R-A36D-312880TCGA-BR-7959-01A-11R-2343-1310100TCGA-IN-8462-01A-11R-2343-135720TCGA-CG-4443-01A-01R-1157-139120TCGA-KB-A93J-01A-11R-A39E-3111240TCGA-HU-A4H3-01A-21R-A251-318820TCGA-RD-A8MV-01A-11R-A36D-3137200TCGA-VQ-A91X-01A-12R-A414-312891TCGA-D7-8575-01A-11R-2343-135541TCGA-BR-8485-01Alam 11Rly2402- 132800TCGA-D7-A748-01A-12R-A32D-311321TCGA-VQ-A91Z-01A-11R-A414-3116900

-g input gene expression file

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-1157-13TCGA-IN-A6RO-01A-12R-A33Y-31TCGA-HU-A4H3-01A-21R-A251-31FGR16.3440811.967395.3508462.2093511.5380215. 240164.5011182.6024376.261761CD3886.8677215.794513.1113421.2407070.86295513.30473.7287081.6739522.675173ITGAL40.269037.3585663.7691252.3878692.3735138.085918.3052833.6227817.025886CX3CL1603.013226.9135320.222384.19526219.0409714.1529513.758856.6753744.050271CEACAM211.8685362.5719170.6108390.6745581.0921273.4835591.1343094.4712740.584159MATK2.283420.8641160.5197762.4420930.7603483.1929511.1618810.3478821.039336CD79B3.4531981.8799572.8221920.5235871.9265923.6517420.8312880.8836431.979214MMP2513.728293.4511481. 1065631.1312170.87873510.431861.4758521.9142842.312993TRAF3IP35.244011.8801860.8752640.7561530.6032513.3250132.3474730.5704621.315916CD477.7469151.8371922.7707611.0781135.20445122.557831.1010715.0661915.41347BTK6.8562354.3622611.4826881.3715991.9812366.911543.1878480.9554991.48269FMO17.1685677.7118173.2231740.9790340.4503071.0934121.0018080.9102041.558515SYT71.15310581.940682.673384191.611282.493940.5103734.4704821.285060.91944TYROBP591.7796338.0271184.813369.18483150.6397480.5691121.09672.4588116. 9793CD220.8192952.5216071.5885050.412590.3872881.1236330.4882440.2580940.713988

Example: Rscript $scriptdir/univariate_cox_batch.r-m metadata_survival_time.tsv\-g deg_gene_exp_tpm.tsv-e EVENT-t TIME-p imm.unicox-- pvalue

Results of batch cox analysis:

VariableTermBetaStandardErrorZPLRTWaldLogRankHRHRlowerHRupperSYT12SYT120.0911210.0194954.6740352.95E-060.0001282.95E-061.80E-061.0954021.0543361.138067CDH2CDH20.0132660.0030144.4018031.07E-050.0019931.07E-052.11E-071.0133541.0073861.019357GPNMBGPNMB0.0027590.0007683.5901180.0003310.0013130.0003310.0004091.0027621.0012531.004274TMIGD3TMIGD30.067880.0193143.5144680.0004410.0012480.0004410.0004191.0702371.030481.111528LINC01094LINC010940.1324410.0403753.2802930.0010370.0022420.0010370.0010261.1416111.0547541.235621SLC22A20PSLC22A20P0.0494150.015833.121650. 0017980.0120650.0017980.0007361.0506561.0185591.083765IGHV4-61IGHV4-610.0017910.0005823.0775730.0020870.008590.0020870.0017421.0017931.0006511.002937IGHV2-5IGHV2-50.0022360.0007373.0349610.0024060.0077820.0024060.0022051.0022381.0007921.003686SERPINA5SERPINA50.0076810.0025583.0024280.0026780.0097990.0026780.0020641.0077111.002671.012776MS4A4AMS4A4A0.014460.005052.8632180.0041940.0084270.0041940.0047221.0145651.0045721.024657FAM83AFAM83A0.0062370.0023682.6334450.0084520.0285230.0084520.0072951.0062561.0015961. 010938IGLV3-9IGLV3-90.0005470.000212.6082810.00910.0394270.00910.0102441.0005471.0001361.000958STARD3STARD30.0009280.0003582.5889130.0096280.0302580.0096280.0067431.0009281.0002251.001631 read this. This article "how to use univariate_cox_batch.r in R language" has been introduced. If you want to master the knowledge of this article, you still need to practice and use it. If you want to know more about the article, please follow the industry information channel.