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obj << /Title 16 0 R /A 13 0 R /Parent 1256 0 R /Prev 11 0 R /Next 19 0 R >> endobj 11 0 obj << /Title 12 0 R /A 9 0 R /Parent 1256 0 R /Prev 7 0 R /Next 15 0 R >> endobj 7 0 obj << /Title 8 0 R /A 5 0 R /Parent 1256 0 R /Prev 3 0 R /Next 11 0 R >> endobj 3 0 obj << /Title 4 0 R /A 1 0 R /Parent 1256 0 R /Next 7 0 R >> endobj 1257 0 obj << /Names [(Doc-Start) 111 0 R (Rfn.AllVariants) 733 0 R (Rfn.AllVariants.Rdash.class) 734 0 R (Rfn.BSgenome) 254 0 R (Rfn.BcfFile) 613 0 R (Rfn.CodingVariants) 735 0 R] /Limits [(Doc-Start) (Rfn.CodingVariants)] >> endobj 1258 0 obj << /Names [(Rfn.CodingVariants.Rdash.class) 736 0 R (Rfn.CollapsedVCF) 688 0 R (Rfn.CollapsedVCF.Rdash.class) 790 0 R (Rfn.DNAStringSet) 257 0 R (Rfn.DataFrame) 847 0 R (Rfn.DataFrameList) 906 0 R] /Limits [(Rfn.CodingVariants.Rdash.class) (Rfn.DataFrameList)] >> endobj 1259 0 obj << /Names [(Rfn.ExpandedVCF) 793 0 R (Rfn.ExpandedVCF.Rdash.class) 794 0 R (Rfn.FaFile) 255 0 R (Rfn.FilterRules) 190 0 R (Rfn.FiveUTRVariants) 743 0 R (Rfn.FiveUTRVariants.Rdash.class) 744 0 R] /Limits [(Rfn.ExpandedVCF) (Rfn.FiveUTRVariants.Rdash.class)] >> endobj 1260 0 obj << /Names [(Rfn.GLtoGP) 266 0 R (Rfn.GLtoGP.1) 14 0 R (Rfn.GRanges) 312 0 R (Rfn.GRanges.Rdash.class) 477 0 R (Rfn.GRangesList) 256 0 R (Rfn.Hits) 314 0 R] /Limits [(Rfn.GLtoGP) (Rfn.Hits)] >> endobj 1261 0 obj << /Names [(Rfn.IntergenicVariants) 745 0 R (Rfn.IntergenicVariants.Rdash.class) 746 0 R (Rfn.IntronVariants) 747 0 R (Rfn.IntronVariants.Rdash.class) 748 0 R (Rfn.MatrixToSnpMatrix) 337 0 R (Rfn.MatrixToSnpMatrix,matrix,DNAStringSet,DNAStringSetList.Rdash.method) 338 0 R] /Limits [(Rfn.IntergenicVariants) (Rfn.MatrixToSnpMatrix,matrix,DNAStringSet,DNAStringSetList.Rdash.method)] >> endobj 1262 0 obj << /Names [(Rfn.MatrixToSnpMatrix.1) 22 0 R (Rfn.MatrixToSnpMatrix.Rdash.deprecated) 339 0 R (Rfn.PolyPhen) 361 0 R (Rfn.PolyPhenDb) 362 0 R (Rfn.PolyPhenDb.Rdash.class) 355 0 R (Rfn.PolyPhenDb.Rdash.class.1) 26 0 R] /Limits [(Rfn.MatrixToSnpMatrix.1) (Rfn.PolyPhenDb.Rdash.class.1)] >> endobj 1263 0 obj << /Names [(Rfn.PolyPhenDbColumns) 380 0 R (Rfn.PolyPhenDbColumns.1) 30 0 R (Rfn.PromoterVariants) 749 0 R (Rfn.PromoterVariants.Rdash.class) 750 0 R (Rfn.RangedData.Rdash.class) 634 0 R (Rfn.Ranges) 311 0 R] /Limits [(Rfn.PolyPhenDbColumns) (Rfn.Ranges)] >> endobj 1264 0 obj << /Names [(Rfn.SIFT) 655 0 R (Rfn.SIFTDb) 656 0 R (Rfn.SIFTDb.Rdash.class) 649 0 R (Rfn.SIFTDb.Rdash.class.1) 62 0 R (Rfn.SIFTDbColumns) 671 0 R (Rfn.SIFTDbColumns.1) 66 0 R] /Limits [(Rfn.SIFT) (Rfn.SIFTDbColumns.1)] >> endobj 1265 0 obj << /Names [(Rfn.ScanVcfParam) 191 0 R (Rfn.ScanVcfParam,ANY.Rdash.method) 619 0 R (Rfn.ScanVcfParam,missing.Rdash.method) 620 0 R (Rfn.ScanVcfParam.Rdash.class) 478 0 R (Rfn.ScanVcfParam.Rdash.class.1) 58 0 R (Rfn.SimpleList) 848 0 R] /Limits [(Rfn.ScanVcfParam) (Rfn.SimpleList)] >> endobj 1266 0 obj << /Names [(Rfn.SnpMatrix) 205 0 R (Rfn.SpliceSiteVariants) 754 0 R (Rfn.SpliceSiteVariants.Rdash.class) 755 0 R (Rfn.SummarizedExperiment) 877 0 R (Rfn.TabixFile) 171 0 R (Rfn.TabixFile.Rdash.class) 597 0 R] /Limits [(Rfn.SnpMatrix) (Rfn.TabixFile.Rdash.class)] >> endobj 1267 0 obj << /Names [(Rfn.ThreeUTRVariants) 756 0 R (Rfn.ThreeUTRVariants.Rdash.class) 757 0 R (Rfn.TranscriptDb) 313 0 R (Rfn.VCF) 841 0 R (Rfn.VCF.Rdash.class) 222 0 R (Rfn.VCF.Rdash.class.1) 82 0 R] /Limits [(Rfn.ThreeUTRVariants) (Rfn.VCF.Rdash.class.1)] >> endobj 1268 0 obj << /Names [(Rfn.VCFHeader) 901 0 R (Rfn.VCFHeader.Rdash.class) 886 0 R (Rfn.VCFHeader.Rdash.class.1) 86 0 R (Rfn.VariantType.Rdash.class) 732 0 R (Rfn.VariantType.Rdash.class.1) 78 0 R (Rfn.[,VCF,ANY,ANY.Rdash.method) 842 0 R] /Limits [(Rfn.VCFHeader) (Rfn.[,VCF,ANY,ANY.Rdash.method)] >> endobj 1269 0 obj << /Names [(Rfn.[,VCF.Rdash.method) 843 0 R (Rfn.[<.Rdash.,VCF,ANY,ANY,VCF.Rdash.method) 844 0 R (Rfn.alt) 779 0 R (Rfn.alt,VCF.Rdash.method) 780 0 R (Rfn.alt<.Rdash.) 781 0 R (Rfn.alt<.Rdash.,CollapsedVCF,CharacterList.Rdash.method) 782 0 R] /Limits [(Rfn.[,VCF.Rdash.method) (Rfn.alt<.Rdash.,CollapsedVCF,CharacterList.Rdash.method)] >> endobj 1270 0 obj << /Names [(Rfn.alt<.Rdash.,CollapsedVCF,DNAStringSetList.Rdash.method) 783 0 R (Rfn.alt<.Rdash.,ExpandedVCF,DNAStringSet.Rdash.method) 785 0 R (Rfn.alt<.Rdash.,ExpandedVCF,character.Rdash.method) 784 0 R (Rfn.bgzip) 189 0 R (Rfn.cbind,VCF.Rdash.method) 786 0 R (Rfn.class:CollapsedVCF) 787 0 R] /Limits [(Rfn.alt<.Rdash.,CollapsedVCF,DNAStringSetList.Rdash.method) (Rfn.class:CollapsedVCF)] >> endobj 1271 0 obj << /Names [(Rfn.class:ExpandedVCF) 788 0 R (Rfn.class:PolyPhenDb) 356 0 R (Rfn.class:SIFTDb) 650 0 R (Rfn.class:VCF) 789 0 R (Rfn.cols,PolyPhenDb.Rdash.method) 357 0 R (Rfn.cols,SIFTDb.Rdash.method) 651 0 R] /Limits [(Rfn.class:ExpandedVCF) (Rfn.cols,SIFTDb.Rdash.method)] >> endobj 1272 0 obj << /Names [(Rfn.contig) 887 0 R (Rfn.contig,VCFHeader.Rdash.method) 888 0 R (Rfn.downstream) 737 0 R (Rfn.downstream,AllVariants.Rdash.method) 738 0 R (Rfn.downstream,PromoterVariants.Rdash.method) 739 0 R (Rfn.downstream<.Rdash.) 740 0 R] /Limits [(Rfn.contig) (Rfn.downstream<.Rdash.)] >> endobj 1273 0 obj << /Names [(Rfn.downstream<.Rdash.,AllVariants.Rdash.method) 741 0 R (Rfn.downstream<.Rdash.,PromoterVariants.Rdash.method) 742 0 R (Rfn.duplicateRSID) 358 0 R (Rfn.expand,CollapsedVCF.Rdash.method) 791 0 R (Rfn.expand,ExpandedVCF.Rdash.method) 792 0 R (Rfn.extractTranscriptsFromGenome) 259 0 R] /Limits [(Rfn.downstream<.Rdash.,AllVariants.Rdash.method) (Rfn.extractTranscriptsFromGenome)] >> endobj 1274 0 obj << /Names [(Rfn.file) 938 0 R (Rfn.filt) 795 0 R (Rfn.filt,VCF.Rdash.method) 796 0 R (Rfn.filt<.Rdash.) 797 0 R (Rfn.filt<.Rdash.,VCF,character.Rdash.method) 798 0 R (Rfn.filterVcf) 145 0 R] /Limits [(Rfn.file) (Rfn.filterVcf)] >> endobj 1275 0 obj << /Names [(Rfn.filterVcf,TabixFile.Rdash.method) 148 0 R (Rfn.filterVcf,character.Rdash.method) 147 0 R (Rfn.filterVcf.1) 2 0 R (Rfn.fixed) 799 0 R (Rfn.fixed,VCF.Rdash.method) 800 0 R (Rfn.fixed,VCFHeader.Rdash.method) 889 0 R] /Limits [(Rfn.filterVcf,TabixFile.Rdash.method) (Rfn.fixed,VCFHeader.Rdash.method)] >> endobj 1276 0 obj << /Names [(Rfn.fixed<.Rdash.) 801 0 R (Rfn.fixed<.Rdash.,VCF,DataFrame.Rdash.method) 802 0 R (Rfn.geno) 803 0 R (Rfn.geno,VCF,ANY.Rdash.method) 804 0 R (Rfn.geno,VCF,character.Rdash.method) 805 0 R (Rfn.geno,VCF,numeric.Rdash.method) 806 0 R] /Limits [(Rfn.fixed<.Rdash.) (Rfn.geno,VCF,numeric.Rdash.method)] >> endobj 1277 0 obj << /Names [(Rfn.geno,VCF.Rdash.method) 807 0 R (Rfn.geno,VCFHeader,ANY.Rdash.method) 808 0 R (Rfn.geno,VCFHeader.Rdash.method) 890 0 R (Rfn.geno<.Rdash.) 809 0 R (Rfn.geno<.Rdash.,VCF,character,matrix.Rdash.method) 810 0 R (Rfn.geno<.Rdash.,VCF,missing,SimpleList.Rdash.method) 812 0 R] /Limits [(Rfn.geno,VCF.Rdash.method) (Rfn.geno<.Rdash.,VCF,missing,SimpleList.Rdash.method)] >> endobj 1278 0 obj << /Names [(Rfn.geno<.Rdash.,VCF,missing,matrix.Rdash.method) 811 0 R (Rfn.geno<.Rdash.,VCF,numeric,matrix.Rdash.method) 813 0 R (Rfn.genome,VCF.Rdash.method) 814 0 R (Rfn.genotypeToSnpMatrix) 198 0 R (Rfn.genotypeToSnpMatrix,CollapsedVCF.Rdash.method) 200 0 R (Rfn.genotypeToSnpMatrix,array.Rdash.method) 199 0 R] /Limits [(Rfn.geno<.Rdash.,VCF,missing,matrix.Rdash.method) (Rfn.genotypeToSnpMatrix,array.Rdash.method)] >> endobj 1279 0 obj << /Names [(Rfn.genotypeToSnpMatrix.1) 6 0 R (Rfn.getSeq) 260 0 R (Rfn.getTranscriptSeqs) 228 0 R (Rfn.getTranscriptSeqs,GRanges,FaFile.Rdash.method) 229 0 R (Rfn.getTranscriptSeqs,GRangesList,BSgenome.Rdash.method) 230 0 R (Rfn.getTranscriptSeqs,GRangesList,FaFile.Rdash.method) 231 0 R] /Limits [(Rfn.genotypeToSnpMatrix.1) (Rfn.getTranscriptSeqs,GRangesList,FaFile.Rdash.method)] >> endobj 1280 0 obj << /Names [(Rfn.getTranscriptSeqs.1) 10 0 R (Rfn.header) 891 0 R (Rfn.header,VCF.Rdash.method) 815 0 R (Rfn.header,VCFHeader.Rdash.method) 892 0 R (Rfn.indexTabix) 503 0 R (Rfn.info) 816 0 R] /Limits [(Rfn.getTranscriptSeqs.1) (Rfn.info)] >> endobj 1281 0 obj << /Names [(Rfn.info,VCF.Rdash.method) 817 0 R (Rfn.info,VCFHeader.Rdash.method) 893 0 R (Rfn.info<.Rdash.) 818 0 R (Rfn.info<.Rdash.,VCF,DataFrame.Rdash.method) 819 0 R (Rfn.keepSeqlevels,VCF,character.Rdash.method) 820 0 R (Rfn.keys,PolyPhenDb.Rdash.method) 359 0 R] /Limits [(Rfn.info,VCF.Rdash.method) (Rfn.keys,PolyPhenDb.Rdash.method)] >> endobj 1282 0 obj << /Names [(Rfn.keys,SIFTDb.Rdash.method) 652 0 R (Rfn.locateVariants) 284 0 R (Rfn.locateVariants,GRanges,GRangesList,AllVariants.Rdash.method) 285 0 R (Rfn.locateVariants,GRanges,GRangesList,CodingVariants.Rdash.method) 286 0 R (Rfn.locateVariants,GRanges,GRangesList,FiveUTRVariants.Rdash.method) 287 0 R (Rfn.locateVariants,GRanges,GRangesList,IntergenicVariants.Rdash.method) 288 0 R] /Limits [(Rfn.keys,SIFTDb.Rdash.method) (Rfn.locateVariants,GRanges,GRangesList,IntergenicVariants.Rdash.method)] >> endobj 1283 0 obj << /Names [(Rfn.locateVariants,GRanges,GRangesList,IntronVariants.Rdash.method) 289 0 R (Rfn.locateVariants,GRanges,GRangesList,PromoterVariants.Rdash.method) 290 0 R (Rfn.locateVariants,GRanges,GRangesList,SpliceSiteVariants.Rdash.method) 291 0 R (Rfn.locateVariants,GRanges,GRangesList,ThreeUTRVariants.Rdash.method) 292 0 R (Rfn.locateVariants,GRanges,GRangesList,VariantType.Rdash.method) 293 0 R (Rfn.locateVariants,GRanges,TranscriptDb,AllVariants.Rdash.method) 294 0 R] /Limits [(Rfn.locateVariants,GRanges,GRangesList,IntronVariants.Rdash.method) (Rfn.locateVariants,GRanges,TranscriptDb,AllVariants.Rdash.method)] >> endobj 1284 0 obj << /Names [(Rfn.locateVariants,GRanges,TranscriptDb,CodingVariants.Rdash.method) 295 0 R (Rfn.locateVariants,GRanges,TranscriptDb,FiveUTRVariants.Rdash.method) 296 0 R (Rfn.locateVariants,GRanges,TranscriptDb,IntergenicVariants.Rdash.method) 297 0 R (Rfn.locateVariants,GRanges,TranscriptDb,IntronVariants.Rdash.method) 298 0 R (Rfn.locateVariants,GRanges,TranscriptDb,PromoterVariants.Rdash.method) 299 0 R (Rfn.locateVariants,GRanges,TranscriptDb,SpliceSiteVariants.Rdash.method) 300 0 R] /Limits [(Rfn.locateVariants,GRanges,TranscriptDb,CodingVariants.Rdash.method) (Rfn.locateVariants,GRanges,TranscriptDb,SpliceSiteVariants.Rdash.method)] >> endobj 1285 0 obj << /Names [(Rfn.locateVariants,GRanges,TranscriptDb,ThreeUTRVariants.Rdash.method) 301 0 R (Rfn.locateVariants,GRanges,TranscriptDb,VariantType.Rdash.method) 302 0 R (Rfn.locateVariants,Ranges,GRangesList,VariantType.Rdash.method) 303 0 R (Rfn.locateVariants,Ranges,TranscriptDb,VariantType.Rdash.method) 304 0 R (Rfn.locateVariants,VCF,GRangesList,VariantType.Rdash.method) 305 0 R (Rfn.locateVariants,VCF,TranscriptDb,VariantType.Rdash.method) 306 0 R] /Limits [(Rfn.locateVariants,GRanges,TranscriptDb,ThreeUTRVariants.Rdash.method) (Rfn.locateVariants,VCF,TranscriptDb,VariantType.Rdash.method)] >> endobj 1286 0 obj << /Names [(Rfn.locateVariants.1) 18 0 R (Rfn.map) 585 0 R (Rfn.mcols<.Rdash.,VCF.Rdash.method) 821 0 R (Rfn.meta) 894 0 R (Rfn.meta,VCFHeader.Rdash.method) 895 0 R (Rfn.metadata,PolyPhenDb.Rdash.method) 360 0 R] /Limits [(Rfn.locateVariants.1) (Rfn.metadata,PolyPhenDb.Rdash.method)] >> endobj 1287 0 obj << /Names [(Rfn.metadata,SIFTDb.Rdash.method) 653 0 R (Rfn.predictCoding) 258 0 R (Rfn.predictCoding,CollapsedVCF,TranscriptDb,ANY,missing.Rdash.method) 408 0 R (Rfn.predictCoding,ExpandedVCF,TranscriptDb,ANY,missing.Rdash.method) 409 0 R (Rfn.predictCoding,GRanges,TranscriptDb,ANY,DNAStringSet.Rdash.method) 410 0 R (Rfn.predictCoding,Ranges,TranscriptDb,ANY,DNAStringSet.Rdash.method) 411 0 R] /Limits [(Rfn.metadata,SIFTDb.Rdash.method) (Rfn.predictCoding,Ranges,TranscriptDb,ANY,DNAStringSet.Rdash.method)] >> endobj 1288 0 obj << /Names [(Rfn.predictCoding.1) 34 0 R (Rfn.probabilityToSnpMatrix) 445 0 R (Rfn.probabilityToSnpMatrix.1) 38 0 R (Rfn.qual) 822 0 R (Rfn.qual,VCF.Rdash.method) 823 0 R (Rfn.qual<.Rdash.) 824 0 R] /Limits [(Rfn.predictCoding.1) (Rfn.qual<.Rdash.)] >> endobj 1289 0 obj << /Names [(Rfn.qual<.Rdash.,VCF,integer.Rdash.method) 825 0 R (Rfn.rbind,VCF.Rdash.method) 826 0 R (Rfn.readVcf) 192 0 R (Rfn.readVcf,TabixFile,character,GRanges.Rdash.method) 468 0 R (Rfn.readVcf,TabixFile,character,GRangesList.Rdash.method) 469 0 R (Rfn.readVcf,TabixFile,character,RangedData.Rdash.method) 471 0 R] /Limits [(Rfn.qual<.Rdash.,VCF,integer.Rdash.method) (Rfn.readVcf,TabixFile,character,RangedData.Rdash.method)] >> endobj 1290 0 obj << /Names [(Rfn.readVcf,TabixFile,character,RangesList.Rdash.method) 472 0 R (Rfn.readVcf,TabixFile,character,ScanVcfParam.Rdash.method) 473 0 R (Rfn.readVcf,TabixFile,character,missing.Rdash.method) 470 0 R (Rfn.readVcf,character,character,ScanVcfParam.Rdash.method) 466 0 R (Rfn.readVcf,character,character,missing.Rdash.method) 465 0 R (Rfn.readVcf,character,missing,missing.Rdash.method) 467 0 R] /Limits [(Rfn.readVcf,TabixFile,character,RangesList.Rdash.method) (Rfn.readVcf,character,missing,missing.Rdash.method)] >> endobj 1291 0 obj << /Names [(Rfn.readVcf.1) 42 0 R (Rfn.readVcfLongForm) 521 0 R (Rfn.readVcfLongForm,TabixFile,character,GRanges.Rdash.method) 525 0 R (Rfn.readVcfLongForm,TabixFile,character,RangedData.Rdash.method) 527 0 R (Rfn.readVcfLongForm,TabixFile,character,RangesList.Rdash.method) 528 0 R (Rfn.readVcfLongForm,TabixFile,character,ScanVcfParam.Rdash.method) 529 0 R] /Limits [(Rfn.readVcf.1) (Rfn.readVcfLongForm,TabixFile,character,ScanVcfParam.Rdash.method)] >> endobj 1292 0 obj << /Names [(Rfn.readVcfLongForm,TabixFile,character,missing.Rdash.method) 526 0 R (Rfn.readVcfLongForm,character,character,ScanVcfParam.Rdash.method) 523 0 R (Rfn.readVcfLongForm,character,character,missing.Rdash.method) 522 0 R (Rfn.readVcfLongForm,character,missing,missing.Rdash.method) 524 0 R (Rfn.readVcfLongForm.1) 46 0 R (Rfn.ref) 827 0 R] /Limits [(Rfn.readVcfLongForm,TabixFile,character,missing.Rdash.method) (Rfn.ref)] >> endobj 1293 0 obj << /Names [(Rfn.ref,VCF.Rdash.method) 828 0 R (Rfn.ref<.Rdash.) 829 0 R (Rfn.ref<.Rdash.,VCF,DNAStringSet.Rdash.method) 830 0 R (Rfn.refLocsToLocalLocs) 436 0 R (Rfn.refLocsToLocalLocs,GRanges,TranscriptDb,missing.Rdash.method) 556 0 R (Rfn.refLocsToLocalLocs,GRanges,missing,GRangesList.Rdash.method) 555 0 R] /Limits [(Rfn.ref,VCF.Rdash.method) (Rfn.refLocsToLocalLocs,GRanges,missing,GRangesList.Rdash.method)] >> endobj 1294 0 obj << /Names [(Rfn.refLocsToLocalLocs.1) 50 0 R (Rfn.reference) 896 0 R (Rfn.reference,VCFHeader.Rdash.method) 897 0 R (Rfn.renameSeqlevels,VCF,character.Rdash.method) 831 0 R (Rfn.rowData,VCF.Rdash.method) 832 0 R (Rfn.rowData<.Rdash.,VCF.Rdash.method) 833 0 R] /Limits [(Rfn.refLocsToLocalLocs.1) (Rfn.rowData<.Rdash.,VCF.Rdash.method)] >> endobj 1295 0 obj << /Names [(Rfn.samples) 898 0 R (Rfn.samples,VCFHeader.Rdash.method) 899 0 R (Rfn.scanBcf) 505 0 R (Rfn.scanTabix) 504 0 R (Rfn.scanVcf) 487 0 R (Rfn.scanVcf,TabixFile,GRanges.Rdash.method) 575 0 R] /Limits [(Rfn.samples) (Rfn.scanVcf,TabixFile,GRanges.Rdash.method)] >> endobj 1296 0 obj << /Names [(Rfn.scanVcf,TabixFile,RangedData.Rdash.method) 577 0 R (Rfn.scanVcf,TabixFile,RangesList.Rdash.method) 578 0 R (Rfn.scanVcf,TabixFile,ScanVcfParam.Rdash.method) 579 0 R (Rfn.scanVcf,TabixFile,missing.Rdash.method) 576 0 R (Rfn.scanVcf,character,ScanVcfParam.Rdash.method) 573 0 R (Rfn.scanVcf,character,missing.Rdash.method) 572 0 R] /Limits [(Rfn.scanVcf,TabixFile,RangedData.Rdash.method) (Rfn.scanVcf,character,missing.Rdash.method)] >> endobj 1297 0 obj << /Names [(Rfn.scanVcf,connection,missing.Rdash.method) 574 0 R (Rfn.scanVcf.1) 54 0 R (Rfn.scanVcfHeader) 580 0 R (Rfn.scanVcfHeader,TabixFile.Rdash.method) 582 0 R (Rfn.scanVcfHeader,character.Rdash.method) 581 0 R (Rfn.select,PolyPhenDb.Rdash.method) 363 0 R] /Limits [(Rfn.scanVcf,connection,missing.Rdash.method) (Rfn.select,PolyPhenDb.Rdash.method)] >> endobj 1298 0 obj << /Names [(Rfn.select,SIFTDb.Rdash.method) 654 0 R (Rfn.seqlevels,VCF.Rdash.method) 834 0 R (Rfn.show,AllVariants.Rdash.method) 751 0 R (Rfn.show,CollapsedVCF.Rdash.method) 835 0 R (Rfn.show,ExpandedVCF.Rdash.method) 836 0 R (Rfn.show,PromoterVariants.Rdash.method) 752 0 R] /Limits [(Rfn.select,SIFTDb.Rdash.method) (Rfn.show,PromoterVariants.Rdash.method)] >> endobj 1299 0 obj << /Names [(Rfn.show,VCF.Rdash.method) 837 0 R (Rfn.show,VCFHeader.Rdash.method) 900 0 R (Rfn.show,VariantType.Rdash.method) 753 0 R (Rfn.snpStats) 221 0 R (Rfn.snpSummary) 681 0 R (Rfn.snpSummary,CollapsedVCF.Rdash.method) 682 0 R] /Limits [(Rfn.show,VCF.Rdash.method) (Rfn.snpSummary,CollapsedVCF.Rdash.method)] >> endobj 1300 0 obj << /Names [(Rfn.snpSummary.1) 70 0 R (Rfn.strand,VCF.Rdash.method) 838 0 R (Rfn.strand<.Rdash.,VCF.Rdash.method) 839 0 R (Rfn.summarizeVariants) 330 0 R (Rfn.summarizeVariants,GRangesList,VCF,VariantType.Rdash.method) 699 0 R (Rfn.summarizeVariants,GRangesList,VCF,function.Rdash.method) 698 0 R] /Limits [(Rfn.snpSummary.1) (Rfn.summarizeVariants,GRangesList,VCF,function.Rdash.method)] >> endobj 1301 0 obj << /Names [(Rfn.summarizeVariants,TranscriptDb,VCF,CodingVariants.Rdash.method) 700 0 R (Rfn.summarizeVariants,TranscriptDb,VCF,FiveUTRVariants.Rdash.method) 701 0 R (Rfn.summarizeVariants,TranscriptDb,VCF,IntronVariants.Rdash.method) 702 0 R (Rfn.summarizeVariants,TranscriptDb,VCF,PromoterVariants.Rdash.method) 703 0 R 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