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functions to migrate from S4Vectors #2

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LiNk-NY opened this issue Sep 19, 2022 · 1 comment
Open

functions to migrate from S4Vectors #2

LiNk-NY opened this issue Sep 19, 2022 · 1 comment
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@LiNk-NY
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enhancement New feature or request

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@LiNk-NY
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LiNk-NY commented Sep 19, 2022

Hi Hervé, @hpages
When you get a chance, can you note the functions you'd like me to move over from S4Vectors?
I am not sure how to generate a list other than with :

library(S4Vectors); cat(paste("- [ ] ", ls(envir = as.environment("package:S4Vectors"), all.names = TRUE), "\n"))
See list here
  • .__C__Annotated
  • .__C__atomic
  • .__C__character_OR_NULL
  • .__C__DataFrame
  • .__C__DataFrame_OR_NULL
  • .__C__DFrame
  • .__C__expression_OR_function
  • .__C__Factor
  • .__C__FilterMatrix
  • .__C__FilterRules
  • .__C__Hits
  • .__C__HitsList
  • .__C__integer_OR_LLint
  • .__C__integer_OR_raw
  • .__C__List
  • .__C__list_OR_List
  • .__C__LLint
  • .__C__NSBS
  • .__C__Pairs
  • .__C__RectangularData
  • .__C__Rle
  • .__C__SelfHits
  • .__C__SimpleList
  • .__C__SortedByQueryHits
  • .__C__SortedByQueryHitsList
  • .__C__SortedByQuerySelfHits
  • .__C__TransposedDataFrame
  • .__C__Vector
  • .__C__vector_OR_factor
  • .__C__vector_OR_Vector
  • .T!:base
  • .T!=:base
  • .T[:base
  • .T[[:base
  • .T[[<-:base
  • .T[<-:base
  • .T&:base
  • .T%in%:base
  • .T<:base
  • .T<=:base
  • .T==:base
  • .T>:base
  • .T>=:base
  • .T$:base
  • .T$<-:base
  • .__T__active:S4Vectors
  • .__T__active<-:S4Vectors
  • .__T__aggregate:stats
  • .__T__anyDuplicated:BiocGenerics
  • .__T__anyNA:base
  • .__T__append:BiocGenerics
  • .__T__as.character:base
  • .__T__as.complex:base
  • .__T__as.data.frame:BiocGenerics
  • .__T__as.env:S4Vectors
  • .__T__as.factor:base
  • .__T__as.integer:base
  • .__T__as.list:base
  • .__T__as.logical:base
  • .__T__as.matrix:base
  • .__T__as.numeric:base
  • .__T__as.raw:base
  • .__T__as.table:base
  • .__T__bindCOLS:S4Vectors
  • .__T__bindROWS:S4Vectors
  • .__T__by:base
  • .__T__c:base
  • .__T__cbind:BiocGenerics
  • .__T__classNameForDisplay:S4Vectors
  • .__T__coerce:methods
  • .__T__colnames:BiocGenerics
  • .__T__colnames<-:base
  • .__T__combineCols:S4Vectors
  • .__T__combineRows:S4Vectors
  • .__T__complete.cases:stats
  • .__T__cor:stats
  • .__T__countLnodeHits:S4Vectors
  • .__T__countMatches:S4Vectors
  • .__T__countRnodeHits:S4Vectors
  • .__T__cov:stats
  • .__T__decode:S4Vectors
  • .__T__dim:base
  • .__T__dimnames:base
  • .__T__dimnames<-:base
  • .__T__do.call:BiocGenerics
  • .__T__droplevels:base
  • .__T__duplicated:BiocGenerics
  • .__T__elementMetadata:S4Vectors
  • .__T__elementMetadata<-:S4Vectors
  • .__T__elementNROWS:S4Vectors
  • .__T__elementType:S4Vectors
  • .__T__end:stats
  • .__T__eval:BiocGenerics
  • .__T__evalSeparately:S4Vectors
  • .__T__expand:S4Vectors
  • .__T__expand.grid:S4Vectors
  • .__T__extractCOLS:S4Vectors
  • .__T__extractROWS:S4Vectors
  • .__T__FactorToClass:S4Vectors
  • .__T__Filter:BiocGenerics
  • .__T__filterRules:S4Vectors
  • .__T__findMatches:S4Vectors
  • .__T__findRun:S4Vectors
  • .__T__first:S4Vectors
  • .__T__first<-:S4Vectors
  • .__T__from:S4Vectors
  • .__T__getListElement:S4Vectors
  • .__T__grep:BiocGenerics
  • .__T__grepl:BiocGenerics
  • .__T__head:utils
  • .__T__horizontal_slot_names:S4Vectors
  • .__T__intersect:BiocGenerics
  • .__T__is.finite:base
  • .__T__is.na:base
  • .__T__is.unsorted:BiocGenerics
  • .__T__isConstant:S4Vectors
  • .__T__isEmpty:S4Vectors
  • .__T__isSorted:S4Vectors
  • .__T__isStrictlySorted:S4Vectors
  • .__T__lapply:BiocGenerics
  • .__T__length:base
  • .__T__lengths:base
  • .__T__levels:base
  • .__T__levels<-:base
  • .__T__makeNakedCharacterMatrixForDisplay:S4Vectors
  • .__T__match:BiocGenerics
  • .__T__max:base
  • .__T__mcols:S4Vectors
  • .__T__mcols<-:S4Vectors
  • .__T__merge:base
  • .__T__mergeROWS:S4Vectors
  • .__T__metadata:S4Vectors
  • .__T__metadata<-:S4Vectors
  • .__T__mstack:S4Vectors
  • .__T__na.exclude:stats
  • .__T__na.omit:stats
  • .__T__names:base
  • .__T__names<-:base
  • .__T__nchar:base
  • .__T__ncol:base
  • .__T__nLnode:S4Vectors
  • .__T__nnode:S4Vectors
  • .__T__normalizeSingleBracketReplacementValue:S4Vectors
  • .__T__nRnode:S4Vectors
  • .__T__nrow:base
  • .__T__nrun:S4Vectors
  • .__T__NSBS:S4Vectors
  • .__T__Ops:base
  • .__T__order:BiocGenerics
  • .__T__parallel_slot_names:S4Vectors
  • .__T__parallelVectorNames:S4Vectors
  • .__T__params:S4Vectors
  • .__T__pcompare:S4Vectors
  • .__T__pcompareRecursively:S4Vectors
  • .__T__rank:BiocGenerics
  • .__T__rbind:BiocGenerics
  • .__T__Reduce:BiocGenerics
  • .__T__relistToClass:S4Vectors
  • .__T__rename:S4Vectors
  • .__T__rep:base
  • .__T__rep.int:base
  • .__T__replaceCOLS:S4Vectors
  • .__T__replaceROWS:S4Vectors
  • .__T__rev:base
  • .__T__revElements:S4Vectors
  • .__T__Rle:S4Vectors
  • .__T__rownames:BiocGenerics
  • .__T__ROWNAMES:S4Vectors
  • .__T__rownames<-:base
  • .__T__ROWNAMES<-:S4Vectors
  • .__T__runLength:S4Vectors
  • .__T__runLength<-:S4Vectors
  • .__T__runmean:S4Vectors
  • .__T__runq:S4Vectors
  • .__T__runsum:S4Vectors
  • .__T__runValue:S4Vectors
  • .__T__runValue<-:S4Vectors
  • .__T__runwtsum:S4Vectors
  • .__T__sameAsPreviousROW:S4Vectors
  • .__T__sapply:BiocGenerics
  • .__T__sd:BiocGenerics
  • .__T__second:S4Vectors
  • .__T__second<-:S4Vectors
  • .__T__selfmatch:S4Vectors
  • .__T__setdiff:BiocGenerics
  • .__T__setequal:base
  • .__T__setListElement:S4Vectors
  • .__T__shiftApply:S4Vectors
  • .__T__show:methods
  • .__T__showAsCell:S4Vectors
  • .__T__sort:BiocGenerics
  • .__T__space:S4Vectors
  • .__T__split:base
  • .__T__splitAsList:S4Vectors
  • .__T__stack:utils
  • .__T__start:stats
  • .__T__subset:base
  • .__T__subsetByFilter:S4Vectors
  • .__T__substr:base
  • .__T__substring:base
  • .__T__summary:base
  • .__T__Summary:base
  • .__T__t:base
  • .__T__tail:utils
  • .__T__to:S4Vectors
  • .__T__transform:base
  • .__T__unfactor:S4Vectors
  • .__T__union:BiocGenerics
  • .__T__unique:BiocGenerics
  • .__T__unlist:base
  • .__T__unname:S4Vectors
  • .__T__unstrsplit:S4Vectors
  • .__T__updateObject:BiocGenerics
  • .__T__values:S4Vectors
  • .__T__values<-:S4Vectors
  • .__T__var:BiocGenerics
  • .__T__vertical_slot_names:S4Vectors
  • .__T__width:BiocGenerics
  • .__T__window:stats
  • .__T__with:base
  • .__T__within:base
  • .__T__xtabs:BiocGenerics
  • .__T__xtfrm:base
  • .__T__zipdown:S4Vectors
  • .__T__zipup:S4Vectors
  • .Call2
  • .Depends
  • %in%
  • active
  • active<-
  • aggregate
  • aggregate.Vector
  • anyDuplicated
  • anyDuplicated.NSBS
  • anyDuplicated.Rle
  • anyDuplicated.Vector
  • append
  • as.character.LLint
  • as.data.frame
  • as.data.frame.Hits
  • as.data.frame.Vector
  • as.env
  • as.factor
  • as.integer.LLint
  • as.list
  • as.list.Vector
  • as.LLint
  • as.logical.LLint
  • as.matrix
  • as.matrix.Vector
  • as.numeric.LLint
  • as.table
  • as.vector.Rle
  • bindCOLS
  • bindROWS
  • breakTies
  • by
  • cbind
  • cbind_mcols_for_display
  • cbind.DataFrame
  • cbind.List
  • cbind.RectangularData
  • classNameForDisplay
  • coerce
  • colnames
  • colnames<-
  • combineCols
  • combineRows
  • combineUniqueCols
  • complete.cases
  • coolcat
  • cor
  • countLnodeHits
  • countMatches
  • countQueryHits
  • countRnodeHits
  • countSubjectHits
  • cov
  • DataFrame
  • decode
  • diff.Rle
  • do.call
  • droplevels
  • droplevels.Factor
  • droplevels.List
  • droplevels.Rle
  • duplicated
  • duplicated.DataFrame
  • duplicated.Vector
  • duplicatedIntegerPairs
  • duplicatedIntegerQuads
  • elementMetadata
  • elementMetadata<-
  • elementNROWS
  • elementType
  • end
  • endoapply
  • eval
  • evalSeparately
  • expand
  • expand.grid
  • extractCOLS
  • extractROWS
  • Factor
  • FactorToClass
  • Filter
  • FilterMatrix
  • filterRules
  • FilterRules
  • findMatches
  • findRun
  • first
  • first<-
  • fold
  • from
  • get_showHeadLines
  • get_showTailLines
  • getListElement
  • grep
  • grepl
  • head
  • head.LLint
  • head.RectangularData
  • head.Vector
  • Hits
  • HitsList
  • horizontal_slot_names
  • I
  • intersect
  • intersect.Vector
  • is.LLint
  • is.unsorted
  • isConstant
  • isEmpty
  • isRedundantHit
  • isSelfHit
  • isSequence
  • isSingleInteger
  • isSingleNumber
  • isSingleNumberOrNA
  • isSingleString
  • isSingleStringOrNA
  • isSorted
  • isStrictlySorted
  • isTRUEorFALSE
  • lapply
  • levels
  • levels.Rle
  • List
  • LLint
  • make_zero_col_DFrame
  • makeClassinfoRowForCompactPrinting
  • makeNakedCharacterMatrixForDisplay
  • makePrettyMatrixForCompactPrinting
  • match
  • matchIntegerPairs
  • matchIntegerQuads
  • mcols
  • mcols<-
  • mean.Rle
  • median.Rle
  • mendoapply
  • merge
  • mergeROWS
  • metadata
  • metadata<-
  • mstack
  • NA_LLint_
  • na.exclude
  • na.omit
  • nchar
  • ncol
  • new2
  • nLnode
  • nnode
  • normalizeDoubleBracketSubscript
  • normalizeSingleBracketReplacementValue
  • normalizeSingleBracketSubscript
  • nRnode
  • nrow
  • nrun
  • NSBS
  • Ops
  • order
  • orderIntegerPairs
  • orderIntegerQuads
  • Pairs
  • parallel_slot_names
  • parallelVectorNames
  • params
  • pc
  • pcompare
  • pcompareRecursively
  • printAtomicVectorInAGrid
  • quantile.Rle
  • queryHits
  • queryLength
  • rank
  • rbind
  • rbind.RectangularData
  • recycleArg
  • recycleCharacterArg
  • recycleIntegerArg
  • recycleLogicalArg
  • recycleNumericArg
  • Reduce
  • relistToClass
  • remapHits
  • rename
  • rep.int
  • replaceCOLS
  • replaceROWS
  • rev
  • rev.Rle
  • rev.Vector
  • revElements
  • Rle
  • rownames
  • ROWNAMES
  • rownames<-
  • ROWNAMES<-
  • runLength
  • runLength<-
  • runmean
  • runq
  • runsum
  • runValue
  • runValue<-
  • runwtsum
  • safeExplode
  • sameAsPreviousROW
  • sapply
  • sd
  • second
  • second<-
  • selectHits
  • SelfHits
  • selfmatch
  • selfmatchIntegerPairs
  • selfmatchIntegerQuads
  • setdiff
  • setdiff.Vector
  • setequal
  • setequal.Vector
  • setListElement
  • setMethods
  • setValidity2
  • shiftApply
  • show
  • showAsCell
  • SimpleList
  • sort
  • sort.DataFrame
  • sort.List
  • sort.Rle
  • sort.Vector
  • space
  • split
  • splitAsList
  • stack
  • start
  • subjectHits
  • subjectLength
  • subset
  • subset.Vector
  • subsetByFilter
  • substr
  • substring
  • summary
  • Summary
  • summary.Hits
  • summary.Rle
  • summary.Vector
  • svn.time
  • t
  • t.DataFrame
  • t.Hits
  • t.HitsList
  • t.TransposedDataFrame
  • tail
  • tail.LLint
  • tail.RectangularData
  • tail.Vector
  • to
  • toListOfIntegerVectors
  • transform
  • transform.DataFrame
  • transform.Vector
  • unfactor
  • union
  • union.Vector
  • unique
  • unique.DataFrame
  • unique.Vector
  • unname
  • unstrsplit
  • updateObject
  • values
  • values<-
  • var
  • vertical_slot_names
  • width
  • window
  • window.LLint
  • window.Vector
  • with
  • within
  • wmsg
  • xtabs
  • zipdown
  • zipup
@LiNk-NY LiNk-NY added the enhancement New feature or request label Sep 19, 2022
@LiNk-NY LiNk-NY self-assigned this Sep 19, 2022
@LiNk-NY
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LiNk-NY commented Dec 30, 2022

Hi Hervé, @hpages
Any hints on what functions are higher priority?
Thanks!

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