| 7d29a0be |
# Generated by roxygen2: do not edit by hand
|
| 5169999d |
export(adjustLogRatio)
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| f296fa95 |
export(annotateTargets)
|
| 0a9b1fac |
export(bootstrapResults)
|
| f8c4e6ef |
export(calculateBamCoverageByInterval)
|
| 7126b212 |
export(calculateLogRatio)
|
| 4635a932 |
export(calculateMappingBiasGatk4)
|
| c21b35de |
export(calculateMappingBiasVcf)
|
| 0a9b1fac |
export(calculatePowerDetectSomatic)
|
| ec6f11d9 |
export(calculateTangentNormal)
|
| 0a9b1fac |
export(callAlterations)
|
| a3a3ebfa |
export(callAlterationsFromSegmentation)
|
| b1e1666f |
export(callAmplificationsInLowPurity)
|
| b92ea48a |
export(callCIN)
|
| 0a9b1fac |
export(callLOH)
|
| 2f5e50c4 |
export(callMutationBurden)
|
| 0a9b1fac |
export(correctCoverageBias)
|
| ea58a451 |
export(createCurationFile)
export(createNormalDatabase)
|
| 0208ae29 |
export(filterIntervals)
|
| 0a9b1fac |
export(filterVcfBasic)
export(filterVcfMuTect)
|
| 5f6178fa |
export(filterVcfMuTect2)
|
| 0a9b1fac |
export(findFocal)
|
| 0810ee52 |
export(findHighQualitySNPs)
|
| 44f86eab |
export(getSexFromCoverage)
|
| 6145e405 |
export(getSexFromVcf)
|
| 0a9b1fac |
export(plotAbs)
export(poolCoverage)
export(predictSomatic)
|
| 10cbaf16 |
export(preprocessIntervals)
|
| 0fda3814 |
export(processMultipleSamples)
|
| 046ee9ac |
export(readAllelicCountsFile)
|
| d05fa238 |
export(readCoverageFile)
|
| 0a9b1fac |
export(readCurationFile)
|
| d0bf5818 |
export(readIntervalFile)
|
| 80773c30 |
export(readLogRatioFile)
|
| ab9bc387 |
export(readSegmentationFile)
|
| 0a9b1fac |
export(runAbsoluteCN)
export(segmentationCBS)
|
| 8cfaf346 |
export(segmentationGATK4)
|
| 0fda3814 |
export(segmentationHclust)
|
| 0a9b1fac |
export(segmentationPSCBS)
|
| 42833704 |
export(setMappingBiasVcf)
|
| 7d29a0be |
export(setPriorVcf)
|
| ea58a451 |
import(DNAcopy)
|
| 0a9b1fac |
import(IRanges)
import(VariantAnnotation)
|
| a80fc213 |
importFrom(Biobase,package.version)
|
| 250a930d |
importFrom(BiocGenerics,score)
|
| 41196656 |
importFrom(BiocGenerics,unstrand)
|
| 046ee9ac |
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNAStringSetList)
|
| 7d29a0be |
importFrom(Biostrings,letterFrequency)
|
| 5d1f0150 |
importFrom(GenomeInfoDb,"genome<-")
|
| 5679e4af |
importFrom(GenomeInfoDb,"seqlengths<-")
|
| 84504fb1 |
importFrom(GenomeInfoDb,"seqlevels<-")
|
| 7d29a0be |
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,genomeStyles)
|
| 4635a932 |
importFrom(GenomeInfoDb,rankSeqlevels)
|
| 84504fb1 |
importFrom(GenomeInfoDb,seqlengths)
|
| a339f472 |
importFrom(GenomeInfoDb,seqlevelsInUse)
|
| 7d29a0be |
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
|
| 41196656 |
importFrom(GenomeInfoDb,sortSeqlevels)
|
| 2b1bc419 |
importFrom(GenomicFeatures,cdsByOverlaps)
|
| f296fa95 |
importFrom(GenomicFeatures,exonsByOverlaps)
importFrom(GenomicFeatures,transcriptsByOverlaps)
|
| 7d29a0be |
importFrom(GenomicRanges,GRanges)
|
| c21b35de |
importFrom(GenomicRanges,GRangesList)
|
| 41196656 |
importFrom(GenomicRanges,tile)
|
| 2b60cf8b |
importFrom(GenomicRanges,tileGenome)
|
| ec6f11d9 |
importFrom(Matrix,tcrossprod)
|
| 7d29a0be |
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,TabixFile)
importFrom(Rsamtools,headerTabix)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanFa)
|
| 41196656 |
importFrom(Rsamtools,scanFaIndex)
|
| 30280c98 |
importFrom(S4Vectors,"%in%")
|
| 7d29a0be |
importFrom(S4Vectors,DataFrame)
|
| 38f2e5f7 |
importFrom(S4Vectors,expand)
|
| c19dd28c |
importFrom(S4Vectors,mcols)
|
| 7d29a0be |
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(SummarizedExperiment,rowRanges)
|
| 46065c94 |
importFrom(VGAM,Coef)
importFrom(VGAM,betabinomial)
importFrom(VGAM,dbetabinom)
|
| ce9822f2 |
importFrom(VGAM,dbetabinom.ab)
|
| 46065c94 |
importFrom(VGAM,vglm)
|
| 7d29a0be |
importFrom(data.table,data.table)
|
| 4635a932 |
importFrom(data.table,dcast)
|
| 653a7a79 |
importFrom(data.table,fread)
|
| 67a695ed |
importFrom(data.table,fwrite)
|
| e2107a3e |
importFrom(data.table,rbindlist)
|
| 4d22136e |
importFrom(futile.logger,appender.tee)
importFrom(futile.logger,flog.appender)
|
| aeb7c9d0 |
importFrom(futile.logger,flog.debug)
|
| 4d22136e |
importFrom(futile.logger,flog.fatal)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.threshold)
importFrom(futile.logger,flog.warn)
|
| 7d29a0be |
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
|
| b47eb36e |
importFrom(ggplot2,coord_trans)
|
| 7d29a0be |
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
|
| b47eb36e |
importFrom(ggplot2,geom_abline)
|
| 4d22136e |
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
|
| 7d29a0be |
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
|
| 4d22136e |
importFrom(ggplot2,labs)
|
| 7d29a0be |
importFrom(ggplot2,scale_alpha_continuous)
|
| 50b46240 |
importFrom(ggplot2,scale_y_sqrt)
|
| 7d29a0be |
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,barplot)
importFrom(graphics,boxplot)
importFrom(graphics,contour)
importFrom(graphics,hist)
importFrom(graphics,image)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,strwidth)
importFrom(graphics,symbols)
importFrom(graphics,text)
|
| b47eb36e |
importFrom(gridExtra,grid.arrange)
|
| 4bb7692f |
importFrom(mclust,Mclust)
importFrom(mclust,emControl)
importFrom(mclust,mclustBIC)
|
| bd374dcb |
importFrom(methods,is)
|
| 36ccafcf |
importFrom(rhdf5,H5Fopen)
|
| 7d29a0be |
importFrom(rtracklayer,import)
importFrom(stats,C)
|
| c19dd28c |
importFrom(stats,aggregate)
|
| 3d43123d |
importFrom(stats,binom.test)
|
| 7d29a0be |
importFrom(stats,complete.cases)
importFrom(stats,cutree)
importFrom(stats,dbeta)
importFrom(stats,dbinom)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,dunif)
|
| b1e1666f |
importFrom(stats,ecdf)
|
| 7d29a0be |
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,loess)
|
| f69711ea |
importFrom(stats,na.omit)
|
| 7d29a0be |
importFrom(stats,pbeta)
|
| b1e1666f |
importFrom(stats,pnorm)
|
| 7d29a0be |
importFrom(stats,predict)
importFrom(stats,runif)
importFrom(stats,t.test)
importFrom(stats,weighted.mean)
|
| 9ef01988 |
importFrom(tools,file_ext)
|
| 8cfaf346 |
importFrom(utils,compareVersion)
|
| 7d29a0be |
importFrom(utils,data)
importFrom(utils,head)
|
| 6357b798 |
importFrom(utils,object.size)
|
| 7d29a0be |
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,tail)
importFrom(utils,write.csv)
|
| 046ee9ac |
importFrom(utils,write.table)
|
