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8 changes: 4 additions & 4 deletions man/ScanVcfParam-class.Rd
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Expand Up @@ -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}.
}
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26 changes: 13 additions & 13 deletions man/VCF-class.Rd
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Expand Up @@ -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.
}

Expand Down Expand Up @@ -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
Expand All @@ -413,7 +413,7 @@
\author{Valerie Obenchain}

\seealso{
\link{GRanges},
\link[GenomicRanges:GRanges-class]{GRanges},
\link[S4Vectors]{DataFrame},
\link[S4Vectors]{SimpleList},
\link[SummarizedExperiment]{RangedSummarizedExperiment},
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4 changes: 2 additions & 2 deletions man/VCFHeader-class.Rd
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Expand Up @@ -143,7 +143,7 @@
}
\item{\code{sample}}{character() vector
}
\item{\code{header}}{\link{DataFrameList}-class
\item{\code{header}}{\link[IRanges:DataFrameList-class]{DataFrameList} class
}
}
}
Expand All @@ -152,7 +152,7 @@

\seealso{
\code{\link{scanVcfHeader}},
\code{\link{DataFrameList}}
\code{\link[IRanges:DataFrameList-class]{DataFrameList}}
}

\examples{
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5 changes: 3 additions & 2 deletions man/VcfFile-class.Rd
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion man/defunct.Rd
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Expand Up @@ -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}}
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14 changes: 7 additions & 7 deletions man/filterVcf-methods.Rd
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Expand Up @@ -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}
Expand All @@ -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
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2 changes: 1 addition & 1 deletion man/indexVcf-method.Rd
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Expand Up @@ -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
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17 changes: 9 additions & 8 deletions man/predictCoding-methods.Rd
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Expand Up @@ -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
Expand All @@ -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
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10 changes: 5 additions & 5 deletions man/readVcf-methods.Rd
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Expand Up @@ -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}}.

Expand Down Expand Up @@ -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}}
}

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8 changes: 4 additions & 4 deletions man/scanVcf-methods.Rd
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Expand Up @@ -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.
}
Expand All @@ -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
Expand Down Expand Up @@ -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{
Expand Down