Man pages for EmmaDann/hexamerModel
Tools for modelling random hexamer primer binding
| add.id | Add region ID |
| add.id.2 | Add region ID |
| all.hexamers | All possible hexamers |
| batch.prob.uniform | Primer probability from batch |
| build.random.base | Random base |
| build.random.hex | Random hexamer |
| compare.spear.real | Quantify correlation of predicted and experimental coverage |
| compute.keqs | Compute association constants |
| compute.primer.usage | Compute primer usage |
| correlate.pred.exp | Correlation of predicted and experimental coverage |
| corr.real | Compute coverage correlation of all sampled regions |
| coverage.yield.delta | Compute difference in yield between batches |
| coverage.yield.single | Compute coverage yield |
| delta.yield.permutation | Compute difference in yield of permuted coverage profile |
| epsilon.minimize.chisq | Max. likelihood estimation of scaling factor epsilon |
| find.rev.pairs | Switch primer and template |
| get.avg.methylation | Compute average methylation of genomic region |
| get.range.methylation | Extract methylation of genomic region |
| hexamerMatrix | Compute all possible nucleotide compositions |
| is.palindrome | Check for palindrome sequences |
| join.pt.data | Build dataframe of primer-template data |
| load.expVSpred.coverage | Load coverage profiles |
| load.kmer.abundance | Load genomic kmer abundance |
| load.modelled.deltaG | Load NN deltaG values |
| load.pt.data | Load primer-template matrix |
| loadPtMatrix | Load primer-template matrix |
| make.base.res.bw | Genomic ranges to base resolution |
| make.cum.dist | Build cumulative distribution of coverage profile |
| make.match.df | Build dataframe of matching primer-template data |
| make_pair_df | Make long dataframe of primer-template counts |
| make_ppm_of_usage | From primer usage to position probability matrix |
| make.predVSexp.range | Merge coverage profiles |
| make.predVSexp.track | Make track of predicted VS experimental coverage |
| make.random.profile | Make random permutation of coverage profile |
| nice.plotTrack | Plot comparison of coverage profiles |
| normalize.coverage | Standard normalize coverage |
| norm.scale.n.yield | Normalize and compute yield |
| plot.batch.accuracy | Plot accuracy of prediction for variable primer... |
| plot.expVSpred.coverage.track | Plot predicted and experimental coverage profiles |
| plot.prediction | Plot predicted coverage VS experimental |
| predict.coverage | Coverage prediction |
| prevalent_nucleotide | Compute most abundant nucleotide in sequence |
| primer.prob | Primer probability |
| random.delta.yield.dist | Random yield |
| random.from.even.2 | Make random permutation of coverage profile for random batch |
| randomize | Compute coverage correlation of random permutations of... |
| rev.comp | Reverse and/or complement sequence |
| simulate.primer.pool | Primer pool simulation |
| smooth.coverage | Kernel smoothing of coverage profiles |
| split.tracks | Split ranges by ID |
| subsetByRegion | Subset by region |
| test.add.id | Test IDs |
