R: Subsetting data from a 'SequenceData', 'SequenceDataSet',...

subsetByCoord {RNAmodR}

R Documentation

Subsetting data from a `SequenceData`, `SequenceDataSet`, `SequenceDataList`, `Modifier` or `ModifierSet` object.

Description

With the subsetByCoord function data from a SequenceData, SequenceDataSet, SequenceDataList, Modifier or ModifierSet object can be subset to positions as defined in coord.

If coord contains a column mod and x is a Modifier object, it will be filtered to identifiers matching the modType of x. To disable this behaviour remove the column mod from coord or set type = NA

labelByCoord functions similarly. It will return a SplitDataFrameList, which matches the dimensions of the aggregated data plus the labels column, which contains logical values to indicate selected positions.

Usage

subsetByCoord(x, coord, ...)

labelByCoord(x, coord, ...)

## S4 method for signature 'Modifier,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'Modifier,GRangesList'
subsetByCoord(x, coord, ...)

## S4 method for signature 'ModifierSet'
subset(x, name, pos = 1L, ...)

## S4 method for signature 'ModifierSet,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'ModifierSet,GRangesList'
subsetByCoord(x, coord, ...)

## S4 method for signature 'Modifier,GRanges'
labelByCoord(x, coord, ...)

## S4 method for signature 'Modifier,GRangesList'
labelByCoord(x, coord, ...)

## S4 method for signature 'ModifierSet,GRanges'
labelByCoord(x, coord, ...)

## S4 method for signature 'ModifierSet,GRangesList'
labelByCoord(x, coord, ...)

## S4 method for signature 'SplitDataFrameList,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceData'
subset(x, name, pos = 1L, ...)

## S4 method for signature 'SequenceData,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceData,GRangesList'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataSet'
subset(x, name, pos = 1L, ...)

## S4 method for signature 'SequenceDataSet,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataSet,GRangesList'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataList'
subset(x, name, pos = 1L, ...)

## S4 method for signature 'SequenceDataList,GRanges'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataList,GRangesList'
subsetByCoord(x, coord, ...)

## S4 method for signature 'SequenceData,GRanges'
labelByCoord(x, coord, ...)

## S4 method for signature 'SequenceData,GRangesList'
labelByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataSet,GRanges'
labelByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataSet,GRangesList'
labelByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataList,GRanges'
labelByCoord(x, coord, ...)

## S4 method for signature 'SequenceDataList,GRangesList'
labelByCoord(x, coord, ...)

Arguments

`x`	a `SequenceData`, `SequenceDataSet`, `SequenceDataList`, `Modifier` or `ModifierSet` object.
`coord`	coordinates of position to subset to. Either a `GRanges` or a `GRangesList` object. For both types the 'Parent' column is expected to match the transcript name.
`...`	Optional parameters: `type`: the modification type used for subsetting. By default this is derived from the `modType(x)`, but it can be overwritten using `type`. It must be a valid shortName for a modification according to `shortName(ModRNAString())` or `shortName(ModDNAString())` (depending on the type of Modifier class) and of course be present in metadata column `mod` of `coord`. To disable subsetting based on type, set `type = NA`. `flanking`: a single integer value to select how many flanking position should be included in the subset (default: `flanking = 0L`). `merge`: `TRUE` or `FALSE`: Should the overlapping selections be merged? This is particular important, if flanking value `!= 0L` are set. (default: `merge = TRUE`). `perTranscript`: `TRUE` or `FALSE`: Should the positions labeled per transcript and not per chromosome? (default: `perTranscript = FALSE`).
`name`	Optional: Limit results to one specific transcript.
`pos`	Optional: Limit results to a specific position.

Value

If 'x' is a

SequenceData or Modifier: a SplitDataFrameList with elments per transcript.
SequenceDataSet, SequenceDataList or ModifierSet: a SimpleList of SplitDataFrameList with elments per transcript.

Examples

data(msi,package="RNAmodR")
mod <- modifications(msi)
coord <- unique(unlist(mod))
coord$score <- NULL
coord$sd <- NULL
subsetByCoord(msi,coord)