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60 lines (59 loc) · 1.78 KB
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# Generated by roxygen2: do not edit by hand
S3method("$",whereAreECDNAs)
S3method("$<-",whereAreECDNAs)
S3method(.DollarNames,whereAreECDNAs)
export(addwhereAreGenomes)
export(buildCellPeakMatrix)
export(callPeak)
export(generatePseudobulk)
export(getAmplicon)
export(getBarcode)
export(getFragment)
export(getwhereAreGenomes)
export(initwhereAreObject)
export(predictECDNACells)
export(quantifyECDNAContent)
export(setGenomeAnnotation)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(Matrix,dgCMatrix)
importFrom(BiocGenerics,which)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,ranges)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(Matrix,Matrix)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,match)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(dplyr,filter)
importFrom(dplyr,pull)
importFrom(dplyr,select)
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slotNames)
importFrom(stats,median)
importFrom(tibble,rownames_to_column)
importFrom(utils,.DollarNames)
importFrom(utils,write.table)