roar (version 1.8.0)

RoarDatasetMultipleAPAFromFiles: Creates a RoarDatasetMultipleAPA object

Description

This function creates an RoarDatasetMultipleAPA object from two lists and a gtf with a suitable annotation of alternative APA sites and exonic structures of genes. A MultipleAPA analysis computes several roar values and p-values for each gene: one for every possible combination of APA-canonical end of a gene (i.e. the end of its last exon). This is more efficient than performing several different ``standard'' roar analyses choosing the PRE and POST portions corresponding to different APAsbecause reads overlaps are computed only once.

Usage

RoarDatasetMultipleAPAFromFiles(treatmentBams, controlBams, gtf)

Arguments

treatmentBams

A list of filenames of bam alignments with data for the treatment condition (by convention it is considered the ``treated'' condition: this simply means that the package will compute roar values (ratios of the m/M) using this condition as the numerator) to be considered.

controlBams

A list of filenames of bam alignments with data for the control condition to be considered.

gtf

A filename of a gtf with coordinates for alternative APA sites and gene exonic structure. This gtf must have three attributes called "gene", "apa" and "type" to distinguish different features. APA should be single bases falling over one of the given genes and need to have the attribute "type" equal to "apa" and the "apa" attribute composed of unambiguous id and the corresponding gene id pasted together with an underscore. The "gene" attributes for these entries should not be initialized. All the studied gene exons need to be reported, in this case the attribute "gene" should contain the gene id (the same one reported for each gene APAs) while "type" should be set to "gene" and "apa" to NA. All apa entries assigned to a gene should have coordinates that falls inside it and every gene that appears should contain at least one APA. A ready-to-go gtf, with coordinates derived from the PolyADB on the human genome (version hg19), is available in the "examples" package directory.

Value

A RoarDatasetMultipleAPA object ready to be analyzed via the other methods.

See Also

RoarDatasetMultipleAPA

Examples

     #rds <- RoarDatasetMultipleAPAFromFiles(treatmentBams, controlBams, gtf)