Man pages for waldronlab/TCGAmisc
TCGA utility functions for data management
| builds | Utilities for working with _HUMAN_ genome builds |
| clinicalNames | Clinical dataset names in TCGA |
| curatedTCGAData-helpers | Helper functions for managing MultiAssayExperiment from... |
| diseaseCodes | TCGA Cancer Disease Codes Table |
| findGRangesCols | Obtain minimum necessary names for the creation of a... |
| generateMap | Create a sampleMap from an experiment list and phenoData... |
| getFileName | Find the file names used in RTCGAToolbox |
| hidden-helpers | A small document for helper functions |
| ID-translation | Translate study identifiers from barcode to UUID and vice... |
| imputeAssay | This function imputes assays values inside a... |
| makeGRangesListFromCopyNumber | Make a GRangesList from TCGA Copy Number data |
| makeGRangesListFromExonFiles | Read exon-level expression files and create a 'GRangesList' |
| mergeColData | Take a MultiAssayExperiment and include curated variables |
| oncoPrintTCGA | OncoPrint for TCGA Mutation Assays |
| sampleTypes | Barcode Sample Type Table |
| simplifyTCGA | Functions to convert rows annotations to ranges and... |
| TCGAbarcode | Parse data from TCGA barcode |
| TCGAbiospec | Extract biospecimen data from the TCGA barcode |
| TCGAprimaryTumors | Select primary tumors from TCGA datasets |
| TCGAsampleSelect | Select samples from barcodes from lookup table |
| TCGAutils-package | TCGAutils: Helper functions for working with TCGA and... |
| trimColData | Minimize the number of variables in colData |
