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docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43) #105

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f3cc08c
fix Rd warnings: \itemize -> \describe and add non-empty labels
vjcitn Jul 18, 2026
e9748a2
bumping version corresponding to Rd changes
vjcitn Jul 18, 2026
ad06705
docs: clarify REFCODON/VARCODON use transcript-strand coordinates (#43)
jmg421 Jul 6, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -3,7 +3,7 @@ Type: Package
Title: Annotation of Genetic Variants
Description: Annotate variants, compute amino acid coding changes,
predict coding outcomes.
Version: 1.59.0
Version: 1.59.2
Authors@R: c(
person("Valerie", "Oberchain", role="aut"),
person("Martin", "Morgan", role="aut"),
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25 changes: 10 additions & 15 deletions man/PolyPhenDb-class.Rd
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Expand Up @@ -22,32 +22,27 @@
\section{Methods}{
In the code below, \code{x} is a \code{PolyPhenDb} object.
\describe{
\item{}{
\code{metadata(x)}:
\item{\code{metadata(x)}}{
Returns \code{x}'s metadata in a data frame.
}
\item{}{
\code{columns(x)}:
\item{\code{columns(x)}}{
Returns the names of the \code{columns} that can be used to subset the
data columns. For column descriptions see \code{?PolyPhenDbColumns}.
}
\item{}{
\code{keys(x)}:
\item{\code{keys(x)}}{
Returns the names of the \code{keys} that can be used to subset the
data rows. The \code{keys} values are the rsid's.
}
\item{}{
\code{select(x, keys = NULL, columns = NULL, ...)}:
Returns a subset of data defined by the character vectors \code{keys}
\item{\code{select(x, keys = NULL, columns = NULL, ...)}}{
Returns a subset of data defined by the character vectors \code{keys}
and \code{columns}. If no \code{keys} are supplied, all rows are
returned. If no \code{columns} are supplied, all columns
are returned. See \code{?PolyPhenDbColumns} for column descriptions.
}
\item{}{
\code{duplicateRSID(x)}:
Returns a named list of duplicate rsid groups. The names are the
\code{keys}, the list elements are the rsid's that have been
reported as having identical chromosome position and alleles and
}
\item{\code{duplicateRSID(x)}}{
Returns a named list of duplicate rsid groups. The names are the
\code{keys}, the list elements are the rsid's that have been
reported as having identical chromosome position and alleles and
therefore translating into the same amino acid residue substitution.
}
}
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14 changes: 5 additions & 9 deletions man/SIFTDb-class.Rd
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Expand Up @@ -21,23 +21,19 @@
\section{Methods}{
In the code below, \code{x} is a \code{SIFTDb} object.
\describe{
\item{}{
\code{metadata(x)}:
\item{\code{metadata(x)}}{
Returns \code{x}'s metadata in a data frame.
}
\item{}{
\code{columns(x)}:
\item{\code{columns(x)}}{
Returns the names of the \code{columns} that can be used to subset the
data columns.
}
\item{}{
\code{keys(x)}:
\item{\code{keys(x)}}{
Returns the names of the \code{keys} that can be used to subset the
data rows. The \code{keys} values are the rsid's.
}
\item{}{
\code{select(x, keys = NULL, columns = NULL, ...)}:
Returns a subset of data defined by the character vectors \code{keys}
\item{\code{select(x, keys = NULL, columns = NULL, ...)}}{
Returns a subset of data defined by the character vectors \code{keys}
and \code{columns}. If no \code{keys} are supplied, all rows are
returned. If no \code{columns} are supplied, all columns
are returned. For column descriptions see \code{?SIFTDbColumns}.
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159 changes: 73 additions & 86 deletions man/VCF-class.Rd
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Expand Up @@ -104,14 +104,13 @@

\section{Constructors}{
\describe{
\item{}{
\code{readVcf(file, genome, param, ..., row.names=TRUE)}
\item{\code{readVcf(file, genome, param, ..., row.names=TRUE)}}{
}
\item{}{
\code{VCF(rowRanges = GRanges(), colData = DataFrame(),
exptData = list(header = VCFHeader()),
fixed = DataFrame(), info = DataFrame(),
geno = SimpleList(), ..., collapsed=TRUE,
\item{\code{VCF(rowRanges, colData, exptData, fixed, info, geno, ...)}}{
\code{VCF(rowRanges = GRanges(), colData = DataFrame(),
exptData = list(header = VCFHeader()),
fixed = DataFrame(), info = DataFrame(),
geno = SimpleList(), ..., collapsed=TRUE,
verbose = FALSE)}
Creates CollapsedVCF when \code{collapsed = TRUE} and an
ExpandedVCF when \code{collapsed = FALSE}.
Expand All @@ -126,123 +125,112 @@
In the following code snippets \code{x} is a CollapsedVCF or ExpandedVCF
object.
\describe{
\item{}{
\code{rowRanges(x, ..., fixed = TRUE)}, \code{rowRanges(x) <- value}:
\item{\code{rowRanges(x, ..., fixed = TRUE)}, \code{rowRanges(x) <- value}}{
Gets or sets the rowRanges. The CHROM, POS, ID, POS and REF fields are
used to create a \code{GRanges} object. The start of the ranges are
defined by POS and the width is equal to the width of the reference
allele REF. The IDs become the rownames. If they are missing (i.e.,
\sQuote{.}) a string of CHROM:POS_REF/ALT is used instead. The
\code{genome} argument is stored in the seqinfo of the \code{GRanges} and
can be accessed with \code{genome(<VCF>)}.
When \code{fixed = TRUE}, REF, ALT, QUAL and FILTER metadata columns are

When \code{fixed = TRUE}, REF, ALT, QUAL and FILTER metadata columns are
displayed as metadata columns. To modify the \code{fixed} fields, use
the \code{fixed<-} setter.
the \code{fixed<-} setter.

One metadata column, \code{paramRangeID}, is included with the
\code{rowRanges}. This ID is meaningful when multiple ranges are
specified in the \code{ScanVcfParam} and distinguishes which records
match each range.

The metadata columns of a VCF object are accessed with the following:
\itemize{
\item{\code{ref(x)}, \code{ref(x) <- value}:
Gets or sets the reference allele (REF). \code{value} must
be a \code{DNAStringSet}.
\describe{
\item{\code{ref(x)}, \code{ref(x) <- value}:}{
Gets or sets the reference allele (REF). \code{value} must
be a \code{DNAStringSet}.
}
\item{\code{alt(x)}, \code{alt(x) <- value}:
Gets or sets the alternate allele data (ALT). When \code{x} is
\item{\code{alt(x)}, \code{alt(x) <- value}:}{
Gets or sets the alternate allele data (ALT). When \code{x} is
a CollapsedVCF, \code{value} must be a \code{DNAStringSetList}
or \code{CompressedCharacterList}. For ExpandedVCF, \code{value}
must be a \code{DNAStringSet} or \code{character}.
}
\item{\code{qual(x)}, \code{qual(x) <- value}:
Returns or sets the quality scores (QUAL). \code{value} must
\item{\code{qual(x)}, \code{qual(x) <- value}:}{
Returns or sets the quality scores (QUAL). \code{value} must
be an \code{numeric(1L)}.
}
\item{\code{filt(x)}, \code{filt(x) <- value}:
Returns or sets the filter data. \code{value} must
\item{\code{filt(x)}, \code{filt(x) <- value}:}{
Returns or sets the filter data. \code{value} must
be a \code{character(1L)}. Names must be one of 'REF', 'ALT',
'QUAL' or 'FILTER'.
}
}
}
\item{}{
\code{mcols(x)}, \code{mcols(x) <- value}:
These methods behave the same as \code{mcols(rowRanges(x))} and
\code{mcols(rowRanges(x)) <- value}. This method does not manage the
fixed fields, 'REF', 'ALT', 'QUAL' or 'FILTER'. To modify those
columns use \code{fixed<-}.
\item{\code{mcols(x)}, \code{mcols(x) <- value}}{
These methods behave the same as \code{mcols(rowRanges(x))} and
\code{mcols(rowRanges(x)) <- value}. This method does not manage the
fixed fields, 'REF', 'ALT', 'QUAL' or 'FILTER'. To modify those
columns use \code{fixed<-}.
}
\item{}{
\code{fixed(x)}, \code{fixed(x) <- value}:
Gets or sets a DataFrame of REF, ALT, QUAL and FILTER only.
Note these fields are displayed as metadata columns with
the rowRanges() data (set to fixed = FALSE to suppress).
\item{\code{fixed(x)}, \code{fixed(x) <- value}}{
Gets or sets a DataFrame of REF, ALT, QUAL and FILTER only.
Note these fields are displayed as metadata columns with
the rowRanges() data (set to fixed = FALSE to suppress).
}
\item{}{
\code{info(x, ..., row.names = TRUE)}, \code{info(x) <- value}:
Gets or sets a DataFrame of INFO variables. Row names are added
if unique and \code{row.names=TRUE}.
\item{\code{info(x, ..., row.names = TRUE)}, \code{info(x) <- value}}{
Gets or sets a DataFrame of INFO variables. Row names are added
if unique and \code{row.names=TRUE}.
}
\item{}{
\code{geno(x, withDimnames=TRUE)}, \code{geno(x) <- value}:
oets a SimpleList of genotype data.
\code{value} is a SimpleList. To replace a single variable in
the SimpleList use \code{geno(x)$variable <- value}; in this
case \code{value} must be a matrix or array. By default
row names are returned; to override specify
\code{geno(vcf, withDimnames=FALSE)}.
\item{\code{geno(x, withDimnames=TRUE)}, \code{geno(x) <- value}}{
Gets a SimpleList of genotype data.
\code{value} is a SimpleList. To replace a single variable in
the SimpleList use \code{geno(x)$variable <- value}; in this
case \code{value} must be a matrix or array. By default
row names are returned; to override specify
\code{geno(vcf, withDimnames=FALSE)}.
}
\item{}{
\code{metadata(x)}:
Gets a \code{list} of experiment-related data. By default this
list includes the \sQuote{header} information from the VCF file.
See the use of \code{header()} for details in extracting
header information.
\item{\code{metadata(x)}}{
Gets a \code{list} of experiment-related data. By default this
list includes the \sQuote{header} information from the VCF file.
See the use of \code{header()} for details in extracting
header information.
}
\item{}{
\code{colData(x)}, \code{colData(x) <- value}:
Gets or sets a \code{DataFrame} of sample-specific information. Each row
represents a sample in the VCF file. \code{value} must be a
\code{DataFrame} with rownames representing the samples in the VCF
\item{\code{colData(x)}, \code{colData(x) <- value}}{
Gets or sets a \code{DataFrame} of sample-specific information. Each row
represents a sample in the VCF file. \code{value} must be a
\code{DataFrame} with rownames representing the samples in the VCF
file.
}
\item{}{
\code{genome(x)}:
\item{\code{genome(x)}}{
Extract the \code{genome} information from the \code{GRanges} object
returned by the \code{rowRanges} accessor.
}
\item{}{
\code{seqlevels(x)}:
\item{\code{seqlevels(x)}}{
Extract the \code{seqlevels} from the \code{GRanges} object
returned by the \code{rowRanges} accessor.
}
\item{}{
\code{strand(x)}:
\item{\code{strand(x)}}{
Extract the \code{strand} from the \code{GRanges} object
returned by the \code{rowRanges} accessor.
}
\item{}{
\code{header(x)}, \code{header(x)<- value}:
\item{\code{header(x)}, \code{header(x)<- value}}{
Get or set the VCF header information. Replacement value
must be a \code{VCFHeader} object. To modify individual elements
use \code{info<-}, \code{geno<-} or \code{meta<-} on a
must be a \code{VCFHeader} object. To modify individual elements
use \code{info<-}, \code{geno<-} or \code{meta<-} on a
\sQuote{VCFHeader} object. See ?\code{VCFHeader} man page for
details.
\itemize{
\item{\code{info(header(x))}}
\item{\code{geno(header(x))}}
\item{\code{meta(header(x))}}
\item{\code{samples(header(x))}}
\itemize{
\item \code{info(header(x))}
\item \code{geno(header(x))}
\item \code{meta(header(x))}
\item \code{samples(header(x))}
}
}
\item{}{\code{vcfFields(x)}
\item{\code{vcfFields(x)}}{
Returns a \code{\link[IRanges]{CharacterList}} of all available VCF
fields, with names of \code{fixed}, \code{info}, \code{geno} and
\code{samples} indicating the four categories. Each element is a
character() vector of available VCF field names within each category.
character() vector of available VCF field names within each category.
}
}
}
Expand All @@ -251,21 +239,21 @@
In the following code \code{x} is a VCF object, and \dots is a list
of VCF objects.
\describe{
\item{}{
\code{x[i, j]}, \code{x[i, j] <- value}: Gets or sets rows and columns.
\item{\code{x[i, j]}, \code{x[i, j] <- value}}{
Gets or sets rows and columns.
\code{i} and \code{j} can be integer or logical vectors. \code{value} is a
replacement \code{VCF} object.
}
\item{}{
\code{subset(x, subset, select, ...)}: Restricts \code{x} by
\item{\code{subset(x, subset, select, ...)}}{
Restricts \code{x} by
evaluating the \code{subset} argument in the scope of
\code{rowData(x)} and \code{info(x)}, and \code{select} in the
context of \code{colData(x)}. The \code{subset} argument restricts
by rows, while the \code{select} argument restricts by column. The
\code{\dots} are passed to the underlying \code{subset()} calls.
}
\item{}{
\code{cbind(...)}, \code{rbind(...)}: \code{cbind} combines objects with
\item{\code{cbind(...)}, \code{rbind(...)}}{
\code{cbind} combines objects with
identical ranges (\code{rowRanges}) but different samples (columns in
\code{assays}). The colnames in \code{colData} must match or an error is
thrown. Columns with duplicate names in \code{fixed}, \code{info} and
Expand All @@ -276,7 +264,7 @@
in \code{colData} must contain the same data. The \sQuote{Samples}
columns in \code{colData} (created by \code{readVcf}) are renamed with a
numeric extension ordered as they were input to \code{rbind} e.g.,
\dQuote{Samples.1, Samples.2, ...} etc.
\dQuote{Samples.1, Samples.2, ...} etc.

\code{metadata} from all objects are combined into a
\code{list} with no name checking.
Expand All @@ -288,18 +276,17 @@
\section{expand}{
In the following code snippets \code{x} is a CollapsedVCF object.
\describe{
\item{}{
\code{expand(x, ..., row.names = FALSE)}:
Expand (unlist) the ALT column of a CollapsedVCF object to one row
\item{\code{expand(x, ..., row.names = FALSE)}}{
Expand (unlist) the ALT column of a CollapsedVCF object to one row
per ALT value. Variables with Number='A' have one value per alternate
allele and are expanded accordingly. The 'AD' genotype field
allele and are expanded accordingly. The 'AD' genotype field
(and any variables with 'Number' set to 'R')
is expanded into REF/ALT pairs. For all other fields, the rows
are replicated to match the elementNROWS of ALT.

The output is an ExpandedVCF with ALT as a \code{DNAStringSet}
The output is an ExpandedVCF with ALT as a \code{DNAStringSet}
or \code{character} (structural variants). By default rownames
are NULL. When \code{row.names=TRUE} the expanded output has
are NULL. When \code{row.names=TRUE} the expanded output has
duplicated rownames corresponding to the original \code{x}.
}
}
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