fngg / an-m6a-related-lncrna-risk-model

R code for article Identification of an m6A-related LncRNA Risk Model for Predicting Prognosis and Directing Treatments in Patients with Colon Adenocarcinoma

an-m6A-related-LncRNA-Risk-Model

1.getClinical.pl：extract clinical information from downloaded TCGA data 2.symbol.pl: translate ENSG id to gene name 3.biotype.pl: differentiate mRNA and lncRNA 4.m6aExp.R: extract the expression level of m6a gene 5.cor.R: identify m6a-related lncRNA 6.mergeTime.R: merge the expression of lncRNA and survival data 7.uniCox.R: identify prognostic m6a lncRNA 8.geneCor.R: correlation analysis of m6a gene and 29 prognostic lncRNA 9.heatmap.R: Heatmap of the expression levels of the 29 m6A-related prognostic lncRNAs in COAD samples and adjacent normal samples 10.riskPlot.R: Risk score distribution of m6A-LPS 11.survial.R: Kaplan–Meier survival analysis 12.ROC.R: receiver operating characteristic curve analysis of the 1-, 2-, and 3-year survival rates 13.cliGroupSur.R: Stratification analysis(investigate the differences in OS of all COAD patients stratified by the clinicopathological variables) 14.TCGAriskDiff_20220505.R: Identify differentially expressed genes(DEGs) between the high- and low-risk groups With sex and age applied as confounding factors 15.GO.R: Gene Ontology (GO) pathway enrichment analysis 16.KEGG.R: Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis 17.volcanoV2.Rmd: visualize the DEGs 18.indep.R: evaluate the independence of m6A-LPS in predicting overall survival (OS) 19.Nomogram.R: establish a nomogram combined two independent risk factors, m6A-LPS and pathologic stage 20.ROC.R: ROC analysis to validate the nomogram in terms of its predictive accuracy 21.Cplot.R: Calibration plots of nomogram 22.TIDE.R: visualize the TIDE prediction scores 23.IPS.R: Immunophenoscore of the high- and low-risk groups 24.pRRophetic.R: IC50 of potential chemotherapeutic drugs