Modifier-functions: Modifier/ModifierSet functions

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

Description

For the Modifier and ModifierSet classes a number of functions are implemented to access the data stored by the object.

The validAggregate and validModification functions check if settings have been modified, after the data was loaded. This potentially invalidates them. To update the data, run the aggregate or the modify function.

Usage

bamfiles(x)

mainScore(x)

modifierType(x)

modType(x)

dataType(x)

sequenceData(x)

sequences(x, ...)

validAggregate(x)

validModification(x)

## S4 method for signature 'Modifier'
show(object)

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

## S4 method for signature 'Modifier'
conditions(object)

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

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

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

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

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

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

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

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

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

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

## S4 method for signature 'Modifier'
sequences(x, modified = FALSE)

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

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

## S4 method for signature 'ModifierSet'
show(object)

## S4 method for signature 'ModifierSet'
bamfiles(x)

## S4 method for signature 'ModifierSet'
conditions(object)

## S4 method for signature 'ModifierSet'
mainScore(x)

## S4 method for signature 'ModifierSet'
modifications(x, perTranscript = FALSE)

## S4 method for signature 'ModifierSet'
modifierType(x)

## S4 method for signature 'ModifierSet'
modType(x)

## S4 method for signature 'ModifierSet'
dataType(x)

## S4 method for signature 'ModifierSet'
ranges(x)

## S4 method for signature 'ModifierSet'
replicates(x)

## S4 method for signature 'ModifierSet'
seqinfo(x)

## S4 method for signature 'ModifierSet'
seqtype(x)

## S4 method for signature 'ModifierSet'
sequences(x, modified = FALSE)

Arguments

x, object	a Modifier or ModifierSet class
...	Additional arguments.
modified	For sequences: TRUE or FALSE: Should the sequences be returned as a ModRNAString/ModDNAString with the found modifications added on top of the RNAString/ DNAString? See combineIntoModstrings.
perTranscript	TRUE or FALSE: Should the positions shown per transcript? (default: perTranscript = FALSE)

Value

• modifierType: a character vector with the appropriate class Name of a Modifier.

• modType: a character vector with the modifications detected by the Modifier class.

• seqtype: a single character value defining if either "RNA" or "DNA" modifications are detected by the Modifier class.

• mainScore: a character vector.

• sequenceData: a SequenceData object.

• modifications: a GRanges or GRangesList object describing the found modifications.

• seqinfo: a Seqinfo object.

• sequences: a RNAStingSet object.

• ranges: a GRangesList object with each element per transcript.

• bamfiles: a BamFileList object.

• validAggregate: TRUE or FALSE. Checks if current settings are the same for which the data was aggregate

• validModification: TRUE or FALSE. Checks if current settings are the same for which modification were found

See Also

settings

Examples

data(msi,package="RNAmodR")
mi <- msi[[1]]
modifierType(mi) # The class name of the Modifier object
modifierType(msi)
seqtype(mi)
modType(mi)
mainScore(mi)
sequenceData(mi)
modifications(mi)
# general accessors
seqinfo(mi)
sequences(mi)
ranges(mi)
bamfiles(mi)

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