| calculate.bij | Calculate the background mutation probability for every... |
| calculate.post.probs | Calculate posterior probability of being a driver |
| compRatio | Cubic spline logistic regression |
| convert.hgnc.to.ensembl | Convert HGNC symbols to Ensembl identifiers using biomaRt |
| convert.seq.to.num | Convert nucleotide sequence to numbers |
| dCG.type | Get mutation type (5-6) of CpG mutations |
| exome | Exome annotation for human genome build NCBI 36/hg18 |
| find.prior.param | Find the maximum likelihood values for the hyperparameters... |
| fit.background.model | Fit background mutation model |
| gene_names | Ensembl names for all genes in the exome |
| generate.sel.exome | Select the part of exome.constants that belongs to a list of... |
| gene.rep.expr | Gene annotation list |
| getA | Compute A - the likelihood of a mutation at every position |
| get.post.probs | Main posterior probability calculation |
| locfdr | Estimation of non-null density |
| lupost2.vec | Likelihood of sample specific mutation rate given the... |
| lupost3.vec | Likelihood of sample specific mutation rate given the... |
| lupost4.vec | Posterior mean of sample-specific mutation rate given the... |
| lupost.vec | Likelihood of mutations in a single gene and sample given the... |
| multiply.p.s.epsilon | Multiply the constants in 'exome.constants' by the relative... |
| multiplyr | Multiply the nonsilent constants in a subsetted... |
| mut.base | Convert nucleotide sequence to column numbers in 'exome.SIFT' |
| mut.lik.change | Calculate change in likelihood due to background mutations |
| mut.type | Get mutation type (transition or transversion) |
| mut.type.converter | Get total counts of mutations for each replication timing,... |
| no.dCG.type | Get mutation type (1-4) of non-CpG mutations |
| number | Convert chromosome names (character) to numeric |
| OV.maf | TCGA Ovarian MAF (Mutation Annotation Format) file |
| preprocess.BM | Pull out sequences, CpG dinucleotide positions, and base... |
| prior | Prior probabilities that each gene is a passenger |
| shuffle.muts | Simulate new dataset |
| sift.col | Retrieve the column from SIFT oject correspoinding to mutated... |
| sift.colA | Retrieve the column from SIFT oject correspoinding to mutated... |
