Man pages for bozdaglab/CTDPathSim2.0
Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine
| estimate_meth_qp | Estimate cell type specific methylation |
| estimate_props_qp | Estimate cell type proportions |
| estimate_stability | This chunk of codes are taken from EDec paper Estimate... |
| find_best_perm | Find best permutation of correlation matrix |
| FindSimFun | Sample-cell line pathway activity-based similarity score |
| GetCellLineDAFun | Cell line-specific differentially aberrated (DA) genes |
| GetCellLineDEFun | Getting cell line-specific differentially expressed (DE)... |
| GetCellLineDMFun | Cell line-specific differentially (DM) genes |
| GetPathFun | Enriched biological pathways |
| GetSampleDEFun | Sample-specific differentially expressed (DE) genes |
| GetSampleDMFun | Sample-specific differentially methylated (DM) genes |
| pat_cnv | Copy number data of patient tumor samples |
| perform_t_tests_all_classes_each_pair | Comparison of each pair of classes |
| perform_t_tests_all_classes_one_vs_rest | Comparison of one class against all others |
| PlotDeconvMethylFun | Correlation plot to show the correlation between the... |
| ProbeToGeneFun | Converting DNA methylation data from probes to genes |
| RunDeconvExprFun | Deconvolution of gene expression of bulk tumor samples |
| RunDeconvMethylFun | Deconvolution of DNA methylation of bulk tumor samples |
| run_edec_stage_1 | This chunk of code from EDec paper Run EDec stage 1... |
| run_edec_stage_2 | This chunk of code from EDec paper Run EDec stage 2 algorithm |
| SampleExprFun | Sample-specific deconvoluted gene expression profile. |
| SampleMethylFun | Sample-specific deconvoluted DNA methylation profile. |
| tTestWithErrorHandling | This chunk of code is from EDec paper Select informative loci... |
