Man pages for peterawe/CMScaller
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
| anno.orgHs | annotation for translating between gene identifiers |
| CMScaller | CMS classification |
| CMSgsa | CMS Gene Set Analysis |
| cohensKappa | Cohen's kappa coefficient |
| corCosine | cosine correlation |
| crcTCGAsubset | colorectal TCGA gene expression data with subtype annotation |
| ematAdjust | matrix row-wise scaling and centering |
| fromTo | translation between human gene identifiers |
| geneSets.CMS | gene sets relevant to Consensus Molecular Subtypes |
| geneSets.CRC | gene sets relevant to Consensus Molecular Subtypes |
| geneSets.reactome | gene sets for exploratory gene set analysis |
| ntp | nearest template prediction |
| ntpMakeTemplates | nearest template prediction templates |
| replaceGeneId | replace matrix gene identifiers |
| subBoxplot | boxplot with data points |
| subCamera | limma/voom camera gene set analysis visualization |
| subDEG | limma/voom differential gene expression analysis |
| subHeatmap | ntp heatmap |
| subMA | MA plot |
| subMDS | MDS plot with class labels |
| subPairs | scatterplots of sample-templates distances |
| subPCA | PCA plot with class labels. |
| subSetNA | sets NTP results to NA based on p-value cutoff |
| subVolcano | volcano plot |
| templates.CMS | development consensus molecular subtype (CMS) templates |
| templates.CRIS | CRC intrinsic subtypes (CRIS) templates |
| templates.MSI | micro-satellite instability templates |
