Man pages for liliulab/gust
Genes Under Selection In Tumors
| append.info | Merge selection coefficients, spatial concentration,... |
| check.gene.consv.all | Retreve fitch rate for each position of a protein. |
| check.gene.mut | Retreve somatic mutations of a gene from one or more tumor... |
| compute.fitch.stats | Compute statistics related to evolutionary conservation |
| compute.selection | Estimate selection coefficients of missense mutations and... |
| compute.selection.stats | Compute statistics related to somatic selection |
| compute.spatial.stats | Compute statistics related to mutational spatial... |
| condense.type | Combine reciprocal mutation types |
| correct.small.sample.bias | Correct biases for genes with too few somatic variants. |
| find.outliers | Find hypo- and hyper-mutated samples |
| find_peaks | Detect mutational hotspots |
| get.exp | Get expected counts of variants for a vector of gene symbols |
| get.opt.genes | Estimate selection coefficients |
| gust | Perform GUST classification of oncogens, tumor suppressor... |
| initialize.gust | Prepare data for GUST classification return a list of data... |
| make.prediction | Predict oncogenes, tumor suppressor genes and passenger... |
| organize.obs | Organize a collection of variants in a gene into counts |
| parse.aggregated.mut | Parse the VCF file to aggregate variants by genes and... |
| plot.multiple | Plot distribution of somatic mutations of multiple genes. |
| plot.mut | Plot distribution of somatic mutations. |
| plot.this.one | Plot distribution of somatic mutations of a gene. |
| prob | optimization function to estimate independent probabilities... |
| prob.joint | optimization function to estimate joint probabilities of... |
| prob.joint.indel | optimization function to estimate joint probabilities of... |
| reformat | Reformat a data frame to be suitable for modeling. |
