From 48917dbdd9f9a678f449a94bb407206204244d6e Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Thu, 16 Oct 2025 22:19:20 -0400 Subject: [PATCH 1/2] add package anchors to cross-refs --- man/ScanVcfParam-class.Rd | 8 ++++---- man/VCF-class.Rd | 26 +++++++++++++------------- man/VCFHeader-class.Rd | 4 ++-- man/VcfFile-class.Rd | 5 +++-- man/defunct.Rd | 2 +- man/filterVcf-methods.Rd | 14 +++++++------- man/indexVcf-method.Rd | 2 +- man/predictCoding-methods.Rd | 17 +++++++++-------- man/readVcf-methods.Rd | 10 +++++----- man/scanVcf-methods.Rd | 8 ++++---- 10 files changed, 49 insertions(+), 47 deletions(-) diff --git a/man/ScanVcfParam-class.Rd b/man/ScanVcfParam-class.Rd index e49683a..098005b 100644 --- a/man/ScanVcfParam-class.Rd +++ b/man/ScanVcfParam-class.Rd @@ -74,10 +74,10 @@ \item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields with no values should be returned. } - \item{which}{A \code{\linkS4class{GRanges}} describing the sequences and - ranges to be queried. Variants whose \code{POS} lies in the interval(s) - \code{[start, end]} are returned. If \code{which} is not specified all - ranges are returned. + \item{which}{A \link[GenomicRanges:GRanges-class]{GRanges} describing the + sequences and ranges to be queried. Variants whose \code{POS} lies in the + interval(s) \code{[start, end]} are returned. If \code{which} is not + specified all ranges are returned. } \item{object}{An instance of class \code{ScanVcfParam}. } diff --git a/man/VCF-class.Rd b/man/VCF-class.Rd index b3320bc..efb8343 100644 --- a/man/VCF-class.Rd +++ b/man/VCF-class.Rd @@ -315,7 +315,7 @@ This function converts the output from the \link[snpStats]{read.plink} function to a \code{VCF} class. \code{from} must be a list of length 3 with named elements "map", "fam" and "genotypes". \code{seqSource} can - be a \code{\link[BSgenome]{BSgenome}} or an \link{FaFile} + be a \code{\link[BSgenome]{BSgenome}} or an \link[Rsamtools]{FaFile} used for reference sequence extraction. } @@ -376,23 +376,23 @@ Slots unique to \code{VCF} and subclasses, \itemize{ - \item \code{fixed}: A \link{DataFrame} containing the REF, ALT, QUAL - and FILTER fields from a VCF file. - \item \code{info}: A \link{DataFrame} containing the INFO fields from - a VCF file. + \item \code{fixed}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing + the REF, ALT, QUAL and FILTER fields from a VCF file. + \item \code{info}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing + the INFO fields from a VCF file. } Slots inherited from \code{RangedSummarizedExperiment}, \itemize{ \item \code{metadata}: A \code{list} containing the file header or other information about the overall experiment. - \item \code{rowRanges}: A \link{GRanges}-class instance defining the - variant ranges and associated metadata columns of REF, ALT, QUAL - and FILTER. While the REF, ALT, QUAL and FILTER fields can - be displayed as metadata columns they cannot be modified with - \code{rowRanges<-}. To modify these fields use \code{fixed<-}. - \item \code{colData}: A \link{DataFrame}-class instance describing the - samples and associated metadata. + \item \code{rowRanges}: A \link[GenomicRanges:GRanges-class]{GRanges} class + instance defining the variant ranges and associated metadata columns + of REF, ALT, QUAL and FILTER. While the REF, ALT, QUAL and FILTER + fields can be displayed as metadata columns they cannot be modified + with \code{rowRanges<-}. To modify these fields use \code{fixed<-}. + \item \code{colData}: A \link[S4Vectors:DataFrame-class]{DataFrame} class + instance describing the samples and associated metadata. \item \code{geno}: The \code{assays} slot from \code{RangedSummarizedExperiment} has been renamed as \code{geno} for the VCF class. This slot contains the genotype information @@ -413,7 +413,7 @@ \author{Valerie Obenchain} \seealso{ - \link{GRanges}, + \link[GenomicRanges:GRanges-class]{GRanges}, \link[S4Vectors]{DataFrame}, \link[S4Vectors]{SimpleList}, \link[SummarizedExperiment]{RangedSummarizedExperiment}, diff --git a/man/VCFHeader-class.Rd b/man/VCFHeader-class.Rd index 51d20c7..622b0d8 100644 --- a/man/VCFHeader-class.Rd +++ b/man/VCFHeader-class.Rd @@ -143,7 +143,7 @@ } \item{\code{sample}}{character() vector } - \item{\code{header}}{\link{DataFrameList}-class + \item{\code{header}}{\link[IRanges:DataFrameList-class]{DataFrameList} class } } } @@ -152,7 +152,7 @@ \seealso{ \code{\link{scanVcfHeader}}, - \code{\link{DataFrameList}} + \code{\link[IRanges:DataFrameList-class]{DataFrameList}} } \examples{ diff --git a/man/VcfFile-class.Rd b/man/VcfFile-class.Rd index 3523680..65d8406 100644 --- a/man/VcfFile-class.Rd +++ b/man/VcfFile-class.Rd @@ -99,14 +99,15 @@ \section{Fields}{ \code{VcfFile} and \code{VcfFileList} classes inherit fields from the - \code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}} + \code{\link[Rsamtools]{TabixFile}} and \code{\link[Rsamtools]{TabixFileList}} classes. } \section{Functions and methods}{ \code{VcfFile} and \code{VcfFileList} classes inherit methods from the - \code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}} + \code{\link[Rsamtools:TabixFile-class]{TabixFile}} and + \code{\link[Rsamtools:TabixFileList-class]{TabixFileList}} classes. ## Opening / closing: diff --git a/man/defunct.Rd b/man/defunct.Rd index 3161db8..4779b35 100644 --- a/man/defunct.Rd +++ b/man/defunct.Rd @@ -79,7 +79,7 @@ \seealso{ \itemize{ - \item \code{\link{expand}} + \item \code{\link[S4Vectors]{expand}} \item \code{\link{filterVcf}} \item \code{\link{genotypeToSnpMatrix}} \item \code{\link[GenomicFeatures]{mapToTranscripts}} diff --git a/man/filterVcf-methods.Rd b/man/filterVcf-methods.Rd index 498c3f8..5368a19 100644 --- a/man/filterVcf-methods.Rd +++ b/man/filterVcf-methods.Rd @@ -20,7 +20,7 @@ } \arguments{ - \item{file}{A \code{character(1)} file path or \code{\link{TabixFile}} + \item{file}{A \code{character(1)} file path or \code{\link[Rsamtools]{TabixFile}} specifying the VCF file to be filtered.} \item{genome}{A \code{character(1)} identifier} @@ -34,14 +34,14 @@ messages should be printed.} \item{index}{A \code{logical(1)} indicating whether the filtered file - should be compressed and indexed (using \code{\link{bgzip}} and - \code{indexTabix}).} + should be compressed and indexed (using \code{\link[Rsamtools]{bgzip}} and + \code{\link[Rsamtools]{indexTabix}}).} - \item{prefilters}{A \code{\link{FilterRules}} instance contains rules for - filtering un-parsed lines of the VCF file.} + \item{prefilters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}} + instance contains rules for filtering un-parsed lines of the VCF file.} - \item{filters}{A \code{\link{FilterRules}} instance contains rules for - filtering fully parsed VCF objects.} + \item{filters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}} + instance contains rules for filtering fully parsed VCF objects.} \item{param}{A \code{\link{ScanVcfParam}} instance restricting input of particular \code{info} or \code{geno} fields, or genomic diff --git a/man/indexVcf-method.Rd b/man/indexVcf-method.Rd index 2282ae8..e0f8078 100644 --- a/man/indexVcf-method.Rd +++ b/man/indexVcf-method.Rd @@ -31,7 +31,7 @@ \details{ If \code{x} is a character vector, assumes they are the path(s) to bgzf-compressed VCF file(s). If an index does not exist, one is - created. VCF files can be compreseed using \code{\link{bgzip}}. A + created. VCF files can be compreseed using \code{\link[Rsamtools]{bgzip}}. A \code{VcfFile} or \code{VcfFileList} is returned. If a \code{VcfFile} or \code{VcfFileList} is given, the index file is diff --git a/man/predictCoding-methods.Rd b/man/predictCoding-methods.Rd index 6bbe61c..f1aecf7 100644 --- a/man/predictCoding-methods.Rd +++ b/man/predictCoding-methods.Rd @@ -21,12 +21,13 @@ } \arguments{ - \item{query}{A \linkS4class{VCF}, \link{IntegerRanges}, \link{GRanges} or - \code{VRanges} instance containing the variants to be annotated. If - \code{query} is a \link[IRanges]{IntegerRanges} or \code{VRanges} it is - coerced to a \link{GRanges}. If a \linkS4class{VCF} is provided the - \code{GRanges} returned by the \code{rowRanges()} accessor will be used. - All metadata columns are ignored. + \item{query}{A \linkS4class{VCF}, \link[IRanges]{IntegerRanges}, + \link[GenomicRanges:GRanges-class]{GRanges} or \code{VRanges} instance + containing the variants to be annotated. If \code{query} is a + \link[IRanges]{IntegerRanges} or \code{VRanges} it is coerced to a + \link[GenomicRanges:GRanges-class]{GRanges}. If a \linkS4class{VCF} is + provided the \code{GRanges} returned by the \code{rowRanges()} accessor will + be used. All metadata columns are ignored. When \code{query} is not a \code{VCF} object a \code{varAllele} must be provided. The \code{varAllele} must be a \code{DNAStringSet} the same length @@ -43,8 +44,8 @@ \link[GenomicFeatures]{TxDb} objects with \code{makeTxDbFromGFF()} in the \code{txdbmaker} package. } - \item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an \link{FaFile} - to be used for sequence extraction. + \item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an + \link[Rsamtools]{FaFile} to be used for sequence extraction. } \item{varAllele}{A \link[Biostrings]{DNAStringSet} containing the variant (alternate) alleles. The length of \code{varAllele} must equal the length diff --git a/man/readVcf-methods.Rd b/man/readVcf-methods.Rd index 6ed0af3..2058d65 100644 --- a/man/readVcf-methods.Rd +++ b/man/readVcf-methods.Rd @@ -51,7 +51,7 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE) \arguments{ \item{file}{A \code{\link{VcfFile}} (synonymous with - \code{\link{TabixFile}}) instance or character() name of the VCF + \code{\link[Rsamtools]{TabixFile}}) instance or character() name of the VCF file to be processed. When ranges are specified in \code{param}, \code{file} must be a \code{\link{VcfFile}}. @@ -268,10 +268,10 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE) \seealso{ \code{\link{indexVcf}}, \code{\link{VcfFile}}, - \code{\link{indexTabix}}, - \code{\link{TabixFile}}, - \code{\link{scanTabix}}, - \code{\link{scanBcf}}, + \code{\link[Rsamtools]{indexTabix}}, + \code{\link[Rsamtools]{TabixFile}}, + \code{\link[Rsamtools]{scanTabix}}, + \code{\link[Rsamtools]{scanBcf}}, \code{\link{expand,CollapsedVCF-method}} } diff --git a/man/scanVcf-methods.Rd b/man/scanVcf-methods.Rd index a1a92a9..94f9fba 100644 --- a/man/scanVcf-methods.Rd +++ b/man/scanVcf-methods.Rd @@ -41,7 +41,7 @@ scanVcf(file, ..., param) \arguments{ \item{file}{For \code{scanVcf} and \code{scanVcfHeader}, the character() - file name, \code{\link{TabixFile}}, or class \code{connection} + file name, \code{\link[Rsamtools]{TabixFile}}, or class \code{connection} (\code{file()} or \code{bgzip()}) of the \sQuote{VCF} file to be processed. } @@ -56,7 +56,7 @@ scanVcf(file, ..., param) \details{ The argument \code{param} allows portions of the file to be input, but requires that the file be bgzip'd and indexed as a - \code{\linkS4class{TabixFile}}. + \code{\link[Rsamtools]{TabixFile}}. \code{scanVcf} with \code{param="missing"} and \code{file="character"} or \code{file="connection"} scan the entire file. With @@ -134,8 +134,8 @@ scanVcf(file, ..., param) \seealso{ \code{\link{readVcf}} - \code{\link{BcfFile}} - \code{\link{TabixFile}} + \code{\link[Rsamtools]{BcfFile}} + \code{\link[Rsamtools]{TabixFile}} } \author{ From 5237e77b556c20af58099042bf8cb74cdb5132f1 Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Wed, 17 Dec 2025 18:32:44 -0500 Subject: [PATCH 2/2] use simplified link for combined class and constructor docs --- man/ScanVcfParam-class.Rd | 2 +- man/VCF-class.Rd | 10 +++++----- man/VCFHeader-class.Rd | 4 ++-- man/VcfFile-class.Rd | 4 ++-- man/filterVcf-methods.Rd | 4 ++-- man/predictCoding-methods.Rd | 4 ++-- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/man/ScanVcfParam-class.Rd b/man/ScanVcfParam-class.Rd index 098005b..826cbc0 100644 --- a/man/ScanVcfParam-class.Rd +++ b/man/ScanVcfParam-class.Rd @@ -74,7 +74,7 @@ \item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields with no values should be returned. } - \item{which}{A \link[GenomicRanges:GRanges-class]{GRanges} describing the + \item{which}{A \link[GenomicRanges]{GRanges} describing the sequences and ranges to be queried. Variants whose \code{POS} lies in the interval(s) \code{[start, end]} are returned. If \code{which} is not specified all ranges are returned. diff --git a/man/VCF-class.Rd b/man/VCF-class.Rd index efb8343..59c8ee3 100644 --- a/man/VCF-class.Rd +++ b/man/VCF-class.Rd @@ -376,9 +376,9 @@ Slots unique to \code{VCF} and subclasses, \itemize{ - \item \code{fixed}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing + \item \code{fixed}: A \link[S4Vectors]{DataFrame} containing the REF, ALT, QUAL and FILTER fields from a VCF file. - \item \code{info}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing + \item \code{info}: A \link[S4Vectors]{DataFrame} containing the INFO fields from a VCF file. } @@ -386,12 +386,12 @@ \itemize{ \item \code{metadata}: A \code{list} containing the file header or other information about the overall experiment. - \item \code{rowRanges}: A \link[GenomicRanges:GRanges-class]{GRanges} class + \item \code{rowRanges}: A \link[GenomicRanges]{GRanges} class instance defining the variant ranges and associated metadata columns of REF, ALT, QUAL and FILTER. While the REF, ALT, QUAL and FILTER fields can be displayed as metadata columns they cannot be modified with \code{rowRanges<-}. To modify these fields use \code{fixed<-}. - \item \code{colData}: A \link[S4Vectors:DataFrame-class]{DataFrame} class + \item \code{colData}: A \link[S4Vectors]{DataFrame} class instance describing the samples and associated metadata. \item \code{geno}: The \code{assays} slot from \code{RangedSummarizedExperiment} has been renamed as \code{geno} @@ -413,7 +413,7 @@ \author{Valerie Obenchain} \seealso{ - \link[GenomicRanges:GRanges-class]{GRanges}, + \link[GenomicRanges]{GRanges}, \link[S4Vectors]{DataFrame}, \link[S4Vectors]{SimpleList}, \link[SummarizedExperiment]{RangedSummarizedExperiment}, diff --git a/man/VCFHeader-class.Rd b/man/VCFHeader-class.Rd index 622b0d8..6fe4c34 100644 --- a/man/VCFHeader-class.Rd +++ b/man/VCFHeader-class.Rd @@ -143,7 +143,7 @@ } \item{\code{sample}}{character() vector } - \item{\code{header}}{\link[IRanges:DataFrameList-class]{DataFrameList} class + \item{\code{header}}{\link[IRanges]{DataFrameList} class } } } @@ -152,7 +152,7 @@ \seealso{ \code{\link{scanVcfHeader}}, - \code{\link[IRanges:DataFrameList-class]{DataFrameList}} + \code{\link[IRanges]{DataFrameList}} } \examples{ diff --git a/man/VcfFile-class.Rd b/man/VcfFile-class.Rd index 65d8406..b579ab3 100644 --- a/man/VcfFile-class.Rd +++ b/man/VcfFile-class.Rd @@ -106,8 +106,8 @@ \section{Functions and methods}{ \code{VcfFile} and \code{VcfFileList} classes inherit methods from the - \code{\link[Rsamtools:TabixFile-class]{TabixFile}} and - \code{\link[Rsamtools:TabixFileList-class]{TabixFileList}} + \code{\link[Rsamtools]{TabixFile}} and + \code{\link[Rsamtools]{TabixFileList}} classes. ## Opening / closing: diff --git a/man/filterVcf-methods.Rd b/man/filterVcf-methods.Rd index 5368a19..1498577 100644 --- a/man/filterVcf-methods.Rd +++ b/man/filterVcf-methods.Rd @@ -37,10 +37,10 @@ should be compressed and indexed (using \code{\link[Rsamtools]{bgzip}} and \code{\link[Rsamtools]{indexTabix}}).} - \item{prefilters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}} + \item{prefilters}{A \code{\link[S4Vectors]{FilterRules-class}} instance contains rules for filtering un-parsed lines of the VCF file.} - \item{filters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}} + \item{filters}{A \code{\link[S4Vectors]{FilterRules-class}} instance contains rules for filtering fully parsed VCF objects.} \item{param}{A \code{\link{ScanVcfParam}} instance restricting input diff --git a/man/predictCoding-methods.Rd b/man/predictCoding-methods.Rd index f1aecf7..4bbf0b6 100644 --- a/man/predictCoding-methods.Rd +++ b/man/predictCoding-methods.Rd @@ -22,10 +22,10 @@ \arguments{ \item{query}{A \linkS4class{VCF}, \link[IRanges]{IntegerRanges}, - \link[GenomicRanges:GRanges-class]{GRanges} or \code{VRanges} instance + \link[GenomicRanges]{GRanges} or \code{VRanges} instance containing the variants to be annotated. If \code{query} is a \link[IRanges]{IntegerRanges} or \code{VRanges} it is coerced to a - \link[GenomicRanges:GRanges-class]{GRanges}. If a \linkS4class{VCF} is + \link[GenomicRanges]{GRanges}. If a \linkS4class{VCF} is provided the \code{GRanges} returned by the \code{rowRanges()} accessor will be used. All metadata columns are ignored.