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

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.

subsetByCoord(x, coord, ...)

labelByCoord(x, coord, ...)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

# S4 method for 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)
#> $SampleSet1
#> SplitDataFrameList of length 6
#> $`2`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.900932
#> 
#> $`4`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.899622
#> 
#> $`6`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.984035
#> 
#> $`7`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 67  0.934553
#> 
#> $`9`
#> DataFrame with 1 row and 1 column
#>       score
#>   <numeric>
#> 7  0.709758
#> 
#> $`11`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.874027
#> 
#> 
#> $SampleSet2
#> SplitDataFrameList of length 6
#> $`2`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.998134
#> 
#> $`4`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.856241
#> 
#> $`6`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.992012
#> 
#> $`7`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 67  0.942905
#> 
#> $`9`
#> DataFrame with 1 row and 1 column
#>       score
#>   <numeric>
#> 7  0.766484
#> 
#> $`11`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.971474
#> 
#> 
#> $SampleSet3
#> SplitDataFrameList of length 6
#> $`2`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.953651
#> 
#> $`4`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.976928
#> 
#> $`6`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 34  0.993128
#> 
#> $`7`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 67  0.943773
#> 
#> $`9`
#> DataFrame with 1 row and 1 column
#>       score
#>   <numeric>
#> 7  0.681451
#> 
#> $`11`
#> DataFrame with 1 row and 1 column
#>        score
#>    <numeric>
#> 35  0.954782
#> 
#>