Man pages for rpiskol/CMString
CMS classification using a selected set of genes that are profiled using the NanoStrin echnology
| checkFeatureIds | detect whether gene expression matrix is labeled with Entrez... |
| classifyCMString | classification of sample gene expression profiles into... |
| exprs.CIT | CIT data set |
| exprs.crc.celllines | CRC cell line data set |
| exprs.MVRM | MVRM data set |
| exprs.Procured | Procured patient data set |
| figClassifyCMS | plot heatmap |
| fillVals | add missing genes to expression matrix. Gene expression for... |
| getAlpha | get alpha parameter |
| getCols | get colors |
| getCvfitList | get list of objects generated using the cv.glmnet function... |
| getExpressionDataSet | load expression data |
| getFit | get glmnet object with the trained classifier |
| getGgColorHue | reproduce ggplot's color hues |
| getLambda | get value of the penalty parameter lambda from... |
| getSignatureGenesPerCMS | extract feature (gene) names/ids for a specific CMS subtype... |
| getSignatureGenesPerCMSFromFit | extract feature (gene) names/ids for a specific CMS subtype... |
| logIfNeeded | apply log2 scale to matrix if needed |
| pieChart | plot pie chart for CMS classification |
| plotContingencyGeneral | plot pie chart for CMS classification |
| randomString | generate random string |
| showAvailableExpressionDataSets | list available expression data |
| subsetSamplesByName | subset samples from the results of the CMS classification... |
| subsetSamplesBySignificance | subset samples from the results of the CMS classification... |
| zscoreVals | z-score expression matrix |
