The ModifierSet class

The ModifierSet class allows multiple Modifier objects to be created from the same annotation and sequence data varying only the bam input files.

In addition the comparison of samples is also done via calling functions on the ModifierSet objects.

The ModifierSet is a virtual class, which derives from the SimpleList class with the slot elementType = "Modifier". The ModifierSet class has to be implemented for each specific analysis.#'

ModifierSet(className, x, annotation, sequences, seqinfo, ...)

# S4 method for list
ModifierSet(
  className,
  x,
  annotation = NULL,
  sequences = NULL,
  seqinfo = NULL,
  ...
)

# S4 method for character
ModifierSet(
  className,
  x,
  annotation = NULL,
  sequences = NULL,
  seqinfo = NULL,
  ...
)

# S4 method for BamFileList
ModifierSet(
  className,
  x,
  annotation = NULL,
  sequences = NULL,
  seqinfo = NULL,
  ...
)

# S4 method for Modifier
ModifierSet(className, x, annotation, sequences, seqinfo, ...)

Arguments

className

The name of the class which should be constructed.

x

the input which can be of the following types

• Modifier: a single Modifier or a list containg only Modifier objects. The input will just be used as elements of the ModifierSet

• BamFileList: a named BamFileList or a list of named BamFileList

• list: a list of one or more types of elements: BamFileList, a named list or named character vector. All elements must be or be coercible to a named BamFileList referencing existing bam files. Valid names are control and treated

annotation

annotation data, which must match the information contained in the BAM files. This is parameter is only required, if x is not a Modifier object.

sequences

sequences matching the target sequences the reads were mapped onto. This must match the information contained in the BAM files. This is parameter is only required, if x is not a Modifier object.

seqinfo

An optional Seqinfo argument or character vector, which can be coerced to one, to subset the sequences to be analyzed on a per chromosome basis.

...

Additional otpional parameters:

• internalBP TRUE or FALSE: should parallelization used internally during creation of each Modifier or should the creation of the Modifier objects be parallalized? (default: internalBP = FALSE). Setting internalBP only makes sense, if the getData function for SequenceData class, the aggregateData or the findMod function contains parallelized code.

All other arguments will be passed onto the Modifier objects.

Value

a ModifierSet object of type className

Creation

The input files have to be provided as a list of elements. Each element in itself must be valid for the creation of Modifier object (Have a look at the man page for more details) and must be named.