Man pages for uclahs-cds/public-R-NanoStringNormCNV
Helper Functions to Normalize NanoString CNV Data
| apply.kd.cna.thresh | Determine the copy number (CN) values from ratios using a... |
| apply.ns.cna.thresh | Determine the copy number (CN) values from pre-defined ratio... |
| calculate.replicate.concordance | Determine copy number concordance across replicate samples |
| calculate.replicate.variance | Determine count variance across replicate samples |
| call.cnas.with.matched.normals | Call CNAs using matched normal references |
| call.cnas.with.pooled.normals | Call CNAs using a pooled normal reference |
| call.copy.number.values | Determine the copy number from counts |
| collapse.genes | Collapse probe counts per gene |
| evaluate.replicates | Perform evaluation using replicates |
| generate.plot.covariates | Generate plot covariate object |
| generate.plot.legend | Generate plot legend object |
| get.ari | Determine the adjusted rand index of a given feature |
| get.cna.thresholds | Determine thresholds for CNA calling |
| get.tumour.normal.ratio | Calculate tumour:normal ratios |
| invariant.probe.norm | Normalize data using invariant probes |
| load.phenodata | Load sample annotation and phenotype information |
| make.cna.densities.plots | Make density plots for normalized counts |
| make.cna.heatmap | Make a heatmap of CNAs |
| make.counts.heatmap | Make a heatmap for NanoString counts |
| make.invariant.probe.plot | Make diagnostic plots for invariant probes |
| make.positive.control.plot | Make heatmaps of positive control correlations |
| make.restriction.fragmentation.plot | Plot the ratios of restriction fragmentation probes |
| make.sample.correlations.heatmap | Make a heatmap of the inter-sample correlations |
| NanoString.DNA.norm | Dataset of normalized NanoString DNA counts from prostate... |
| NanoString.DNA.raw | Dataset of raw NanoString DNA counts from prostate cancer... |
| normalize.global | Wrapper function to normalize raw data, globally |
| normalize.per.chip | Wrapper function to normalize raw data, per cartridge |
| PhenoData | Dataset of sample annotation and phenotype information for 65... |
| positive.control.qc | Perform QAQC using positive controls |
| process.xy.probes | Processes sex chromosome probes |
| restriction.fragmentation.qc | Perform QAQC using restriction fragmentation controls |
| tumour.normal.ratio.to.cn.state | Convert tumour:normal count ratios into discrete copy number... |
| visualize.results | visualize results |
