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add package anchors to cross-refs
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‎man/ScanVcfParam-class.Rd‎

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\item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields
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with no values should be returned.
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}
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\item{which}{A \code{\linkS4class{GRanges}} describing the sequences and
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ranges to be queried. Variants whose \code{POS} lies in the interval(s)
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\code{[start, end]} are returned. If \code{which} is not specified all
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ranges are returned.
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\item{which}{A \link[GenomicRanges:GRanges-class]{GRanges} describing the
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sequences and ranges to be queried. Variants whose \code{POS} lies in the
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interval(s) \code{[start, end]} are returned. If \code{which} is not
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specified all ranges are returned.
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}
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\item{object}{An instance of class \code{ScanVcfParam}.
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}

‎man/VCF-class.Rd‎

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@@ -315,7 +315,7 @@
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This function converts the output from the \link[snpStats]{read.plink}
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function to a \code{VCF} class. \code{from} must be a list of length 3
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with named elements "map", "fam" and "genotypes". \code{seqSource} can
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be a \code{\link[BSgenome]{BSgenome}} or an \link{FaFile}
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be a \code{\link[BSgenome]{BSgenome}} or an \link[Rsamtools]{FaFile}
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used for reference sequence extraction.
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}
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@@ -376,23 +376,23 @@
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Slots unique to \code{VCF} and subclasses,
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\itemize{
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\item \code{fixed}: A \link{DataFrame} containing the REF, ALT, QUAL
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and FILTER fields from a VCF file.
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\item \code{info}: A \link{DataFrame} containing the INFO fields from
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a VCF file.
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\item \code{fixed}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing
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the REF, ALT, QUAL and FILTER fields from a VCF file.
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\item \code{info}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing
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the INFO fields from a VCF file.
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}
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Slots inherited from \code{RangedSummarizedExperiment},
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\itemize{
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\item \code{metadata}: A \code{list} containing the
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file header or other information about the overall experiment.
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\item \code{rowRanges}: A \link{GRanges}-class instance defining the
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variant ranges and associated metadata columns of REF, ALT, QUAL
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and FILTER. While the REF, ALT, QUAL and FILTER fields can
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be displayed as metadata columns they cannot be modified with
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\code{rowRanges<-}. To modify these fields use \code{fixed<-}.
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\item \code{colData}: A \link{DataFrame}-class instance describing the
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samples and associated metadata.
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\item \code{rowRanges}: A \link[GenomicRanges:GRanges-class]{GRanges} class
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instance defining the variant ranges and associated metadata columns
391+
of REF, ALT, QUAL and FILTER. While the REF, ALT, QUAL and FILTER
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fields can be displayed as metadata columns they cannot be modified
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with \code{rowRanges<-}. To modify these fields use \code{fixed<-}.
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\item \code{colData}: A \link[S4Vectors:DataFrame-class]{DataFrame} class
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instance describing the samples and associated metadata.
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\item \code{geno}: The \code{assays} slot from
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\code{RangedSummarizedExperiment} has been renamed as \code{geno}
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for the VCF class. This slot contains the genotype information
@@ -413,7 +413,7 @@
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\author{Valerie Obenchain}
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\seealso{
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\link{GRanges},
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\link[GenomicRanges:GRanges-class]{GRanges},
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\link[S4Vectors]{DataFrame},
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\link[S4Vectors]{SimpleList},
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\link[SummarizedExperiment]{RangedSummarizedExperiment},

‎man/VCFHeader-class.Rd‎

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@@ -143,7 +143,7 @@
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}
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\item{\code{sample}}{character() vector
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}
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\item{\code{header}}{\link{DataFrameList}-class
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\item{\code{header}}{\link[IRanges:DataFrameList-class]{DataFrameList} class
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}
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}
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}
@@ -152,7 +152,7 @@
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\seealso{
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\code{\link{scanVcfHeader}},
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\code{\link{DataFrameList}}
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\code{\link[IRanges:DataFrameList-class]{DataFrameList}}
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}
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\examples{

‎man/VcfFile-class.Rd‎

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\section{Fields}{
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\code{VcfFile} and \code{VcfFileList} classes inherit fields from the
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\code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}}
102+
\code{\link[Rsamtools]{TabixFile}} and \code{\link[Rsamtools]{TabixFileList}}
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classes.
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}
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\section{Functions and methods}{
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\code{VcfFile} and \code{VcfFileList} classes inherit methods from the
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\code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}}
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\code{\link[Rsamtools:TabixFile-class]{TabixFile}} and
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\code{\link[Rsamtools:TabixFileList-class]{TabixFileList}}
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classes.
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## Opening / closing:

‎man/defunct.Rd‎

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\seealso{
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\itemize{
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\item \code{\link{expand}}
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\item \code{\link[S4Vectors]{expand}}
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\item \code{\link{filterVcf}}
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\item \code{\link{genotypeToSnpMatrix}}
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\item \code{\link[GenomicFeatures]{mapToTranscripts}}

‎man/filterVcf-methods.Rd‎

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}
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\arguments{
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\item{file}{A \code{character(1)} file path or \code{\link{TabixFile}}
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\item{file}{A \code{character(1)} file path or \code{\link[Rsamtools]{TabixFile}}
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specifying the VCF file to be filtered.}
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\item{genome}{A \code{character(1)} identifier}
@@ -34,14 +34,14 @@
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messages should be printed.}
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\item{index}{A \code{logical(1)} indicating whether the filtered file
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should be compressed and indexed (using \code{\link{bgzip}} and
38-
\code{indexTabix}).}
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should be compressed and indexed (using \code{\link[Rsamtools]{bgzip}} and
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\code{\link[Rsamtools]{indexTabix}}).}
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40-
\item{prefilters}{A \code{\link{FilterRules}} instance contains rules for
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filtering un-parsed lines of the VCF file.}
40+
\item{prefilters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}}
41+
instance contains rules for filtering un-parsed lines of the VCF file.}
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43-
\item{filters}{A \code{\link{FilterRules}} instance contains rules for
44-
filtering fully parsed VCF objects.}
43+
\item{filters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}}
44+
instance contains rules for filtering fully parsed VCF objects.}
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4646
\item{param}{A \code{\link{ScanVcfParam}} instance restricting input
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of particular \code{info} or \code{geno} fields, or genomic

‎man/indexVcf-method.Rd‎

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\details{
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If \code{x} is a character vector, assumes they are the path(s) to
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bgzf-compressed VCF file(s). If an index does not exist, one is
34-
created. VCF files can be compreseed using \code{\link{bgzip}}. A
34+
created. VCF files can be compreseed using \code{\link[Rsamtools]{bgzip}}. A
3535
\code{VcfFile} or \code{VcfFileList} is returned.
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3737
If a \code{VcfFile} or \code{VcfFileList} is given, the index file is

‎man/predictCoding-methods.Rd‎

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}
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\arguments{
24-
\item{query}{A \linkS4class{VCF}, \link{IntegerRanges}, \link{GRanges} or
25-
\code{VRanges} instance containing the variants to be annotated. If
26-
\code{query} is a \link[IRanges]{IntegerRanges} or \code{VRanges} it is
27-
coerced to a \link{GRanges}. If a \linkS4class{VCF} is provided the
28-
\code{GRanges} returned by the \code{rowRanges()} accessor will be used.
29-
All metadata columns are ignored.
24+
\item{query}{A \linkS4class{VCF}, \link[IRanges]{IntegerRanges},
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\link[GenomicRanges:GRanges-class]{GRanges} or \code{VRanges} instance
26+
containing the variants to be annotated. If \code{query} is a
27+
\link[IRanges]{IntegerRanges} or \code{VRanges} it is coerced to a
28+
\link[GenomicRanges:GRanges-class]{GRanges}. If a \linkS4class{VCF} is
29+
provided the \code{GRanges} returned by the \code{rowRanges()} accessor will
30+
be used. All metadata columns are ignored.
3031

3132
When \code{query} is not a \code{VCF} object a \code{varAllele} must be
3233
provided. The \code{varAllele} must be a \code{DNAStringSet} the same length
@@ -43,8 +44,8 @@
4344
\link[GenomicFeatures]{TxDb} objects with
4445
\code{makeTxDbFromGFF()} in the \code{txdbmaker} package.
4546
}
46-
\item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an \link{FaFile}
47-
to be used for sequence extraction.
47+
\item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an
48+
\link[Rsamtools]{FaFile} to be used for sequence extraction.
4849
}
4950
\item{varAllele}{A \link[Biostrings]{DNAStringSet} containing the variant
5051
(alternate) alleles. The length of \code{varAllele} must equal the length

‎man/readVcf-methods.Rd‎

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@@ -51,7 +51,7 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE)
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\arguments{
5353
\item{file}{A \code{\link{VcfFile}} (synonymous with
54-
\code{\link{TabixFile}}) instance or character() name of the VCF
54+
\code{\link[Rsamtools]{TabixFile}}) instance or character() name of the VCF
5555
file to be processed. When ranges are specified in \code{param},
5656
\code{file} must be a \code{\link{VcfFile}}.
5757

@@ -268,10 +268,10 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE)
268268
\seealso{
269269
\code{\link{indexVcf}},
270270
\code{\link{VcfFile}},
271-
\code{\link{indexTabix}},
272-
\code{\link{TabixFile}},
273-
\code{\link{scanTabix}},
274-
\code{\link{scanBcf}},
271+
\code{\link[Rsamtools]{indexTabix}},
272+
\code{\link[Rsamtools]{TabixFile}},
273+
\code{\link[Rsamtools]{scanTabix}},
274+
\code{\link[Rsamtools]{scanBcf}},
275275
\code{\link{expand,CollapsedVCF-method}}
276276
}
277277

‎man/scanVcf-methods.Rd‎

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@@ -41,7 +41,7 @@ scanVcf(file, ..., param)
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4242
\arguments{
4343
\item{file}{For \code{scanVcf} and \code{scanVcfHeader}, the character()
44-
file name, \code{\link{TabixFile}}, or class \code{connection}
44+
file name, \code{\link[Rsamtools]{TabixFile}}, or class \code{connection}
4545
(\code{file()} or \code{bgzip()}) of the \sQuote{VCF} file to be
4646
processed.
4747
}
@@ -56,7 +56,7 @@ scanVcf(file, ..., param)
5656
\details{
5757
The argument \code{param} allows portions of the file to be input, but
5858
requires that the file be bgzip'd and indexed as a
59-
\code{\linkS4class{TabixFile}}.
59+
\code{\link[Rsamtools]{TabixFile}}.
6060
6161
\code{scanVcf} with \code{param="missing"} and \code{file="character"}
6262
or \code{file="connection"} scan the entire file. With
@@ -134,8 +134,8 @@ scanVcf(file, ..., param)
134134

135135
\seealso{
136136
\code{\link{readVcf}}
137-
\code{\link{BcfFile}}
138-
\code{\link{TabixFile}}
137+
\code{\link[Rsamtools]{BcfFile}}
138+
\code{\link[Rsamtools]{TabixFile}}
139139
}
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141141
\author{

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