Package index

All functions

GenomicFiles class:GenomicFiles GenomicFiles-class GenomicFiles,GenomicRanges_OR_GRangesList,character-method GenomicFiles,GenomicRanges_OR_GRangesList,List-method GenomicFiles,GenomicRanges_OR_GRangesList,list-method GenomicFiles,missing,ANY-method GenomicFiles,missing,missing-method files<- files files,GenomicFiles-method files<-,GenomicFiles,character-method files<-,GenomicFiles,List-method dimnames<-,GenomicFiles,list-method colData<-,GenomicFiles,DataFrame-method [,GenomicFiles,ANY,ANY-method [,GenomicFiles,ANY,ANY,ANY-method show,GenomicFiles-method

GenomicFiles objects

GenomicFiles-deprecated getVCFPath

Deprecated functions in package ‘GenomicFiles’

class:VcfStack VcfStack-class RangedVcfStack-class VcfStack RangedVcfStack colnames,VcfStack-method rownames,VcfStack-method dimnames,VcfStack-method files,VcfStack-method files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method files<-,VcfStack,VcfFileList-method seqinfo,VcfStack-method seqinfo<-,VcfStack-method seqinfo<-,RangedVcfStack-method seqlevelsStyle<-,VcfStack-method seqlevelsStyle<-,RangedVcfStack-method colData,VcfStack-method colData<-,VcfStack,DataFrame-method rowRanges,RangedVcfStack-method rowRanges<-,RangedVcfStack,GRanges-method vcfFields,VcfStack-method assay,VcfStack,ANY-method assay,RangedVcfStack,ANY-method readVcfStack show,VcfStack-method [,VcfStack,ANY,ANY-method [,VcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method [,RangedVcfStack,ANY,ANY,ANY-method paths1kg dim,VcfStack-method

VcfStack and RangedVcfStack Objects

pack(<GRanges>)

Range transformations of a GenomicRanges object for optimal file queries.

reduceByFile(<GRanges>,<ANY>) reduceByFile(<GRangesList>,<ANY>) reduceByFile(<GenomicFiles>,<missing>) reduceFiles()

Parallel computations by files

reduceByRange(<GRanges>,<ANY>) reduceByRange(<GRangesList>,<ANY>) reduceByRange(<GenomicFiles>,<missing>) reduceRanges()

Parallel computations by ranges

reduceByYield() REDUCEsampler()

Iterate through a BAM (or other) file, reducing output to a single result.

registerFileType() findTypeRegistry() makeFileType()

Functions for creating and searching a registry of file types.

unpack(<list>,<GRangesList>) unpack(<List>,<GRangesList>)

Un-pack results obtained with a pack()ed group of ranges