Man pages for liliulab/gust
Genes Under Selection In Tumors

append.infoMerge selection coefficients, spatial concentration,...
check.gene.consv.allRetreve fitch rate for each position of a protein.
check.gene.mutRetreve somatic mutations of a gene from one or more tumor...
compute.fitch.statsCompute statistics related to evolutionary conservation
compute.selectionEstimate selection coefficients of missense mutations and...
compute.selection.statsCompute statistics related to somatic selection
compute.spatial.statsCompute statistics related to mutational spatial...
condense.typeCombine reciprocal mutation types
correct.small.sample.biasCorrect biases for genes with too few somatic variants.
find.outliersFind hypo- and hyper-mutated samples
find_peaksDetect mutational hotspots
get.expGet expected counts of variants for a vector of gene symbols
get.opt.genesEstimate selection coefficients
gustPerform GUST classification of oncogens, tumor suppressor...
initialize.gustPrepare data for GUST classification return a list of data...
make.predictionPredict oncogenes, tumor suppressor genes and passenger...
organize.obsOrganize a collection of variants in a gene into counts
parse.aggregated.mutParse the VCF file to aggregate variants by genes and...
plot.multiplePlot distribution of somatic mutations of multiple genes.
plot.mutPlot distribution of somatic mutations.
plot.this.onePlot distribution of somatic mutations of a gene.
proboptimization function to estimate independent probabilities...
prob.jointoptimization function to estimate joint probabilities of...
prob.joint.indeloptimization function to estimate joint probabilities of...
reformatReformat a data frame to be suitable for modeling.
liliulab/gust documentation built on Jan. 20, 2020, 12:07 a.m.