aggregate: Aggregate data per positions

In RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

Description

The aggregate function is defined for each SequenceData object and can be used directly on a SequenceData object or indirectly via a Modifier object.

For the letter the call is redirect to the SequenceData object, the result summarized as defined for the individual Modifier class and stored in the aggregate slot of the Modifier object. The data is then used for subsequent tasks, such as search for modifications and visualization of the results.

The summarization is implemented in the aggregateData for each type of Modifier class. The stored data from the aggregate slot can be retrieved using the getAggregateData function.

Whether the aggrgeated data is already present in the aggregate slot can be checked using the hasAggregateData function.

For SequenceDataSet, SequenceDataList and ModfierSet classes wrapper of the aggregate function exist as well.

Usage

aggregate(x, ...)

aggregateData(x, ...)

getAggregateData(x)

hasAggregateData(x)

## S4 method for signature 'SequenceData'
aggregate(x, condition = c())

## S4 method for signature 'SequenceData'
aggregateData(x, condition)

## S4 method for signature 'SequenceDataSet'
aggregate(x, condition = "Treated")

## S4 method for signature 'SequenceDataList'
aggregate(x, condition = "Treated")

## S4 method for signature 'Modifier'
aggregate(x, force = FALSE)

## S4 method for signature 'Modifier'
aggregateData(x)

## S4 method for signature 'Modifier'
getAggregateData(x)

## S4 method for signature 'Modifier'
hasAggregateData(x)

## S4 method for signature 'ModifierSet'
aggregate(x, force = FALSE)

Arguments

x	a SequenceData, SequenceDataSet, SequenceDataList, Modifier or ModfierSet object.
...	additional arguments
condition	character value, which selects, for which condition the data should be aggregated. One of the following values: Both, Control, Treated
force	whether to recreate the aggregated data, if it is already stored inside the Modifier object.

Value

• aggregate: for SequenceData object the aggregated data is returned as a SplitDataFrameList with an element per transcript, whereas for a Modifier the modified input object is returned, containing the aggregated data, which can be accessed using getAggregateData.

• getAggregateData: only for Modifier: a SplitDataFrameList with an element per transcript is returned. If the aggregated data is not stored in the object, it is generated on the fly, but does not persist.

• hasAggregateData: TRUE or FALSE. Does the Modifier object already contain aggregated data?

If 'x' is a

• SequenceData a SplitDataFrameList with elments per transcript.

• SequenceDataSet or SequenceDataList a SimpleList with SplitDataFrameList as elements.

• Modifier or ModifierSet an updated Modifier object. The data can be accessed by using the aggregateData function.

Examples

data(e5sd,package="RNAmodR")
data(msi,package="RNAmodR")
# modify() triggers the search for modifications in the data contained in
# the Modifier or ModifierSet object
sdfl <- aggregate(e5sd)
mi <- aggregate(msi[[1]])

RNAmodR documentation built on Dec. 15, 2020, 2 a.m.