roar (version 1.4.0)

RoarDatasetFromFiles: Creates a RoarDataset object

Description

This function creates an RoarDataset object from two list and a gtf with a suitable annotation of alternative APA sites.

Usage

RoarDatasetFromFiles(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 the portions of transcripts that has to be considered pertaining to the short (or long) isoform. This gtf must have an attribute called "gene_id" that ends with "_PRE" or "_POST" to address respectively the short and the long isoform. A ready-to-go gtf, with coordinates derived from the PolyADB on the human genome (version hg19), is available in the "examples" package directory. An element in the annotation is considered "PRE" (i.e. common to the short and long isoform of the transcript) if its gene_id feature in the gtf ends with "_PRE". If it ends with "_POST" it is considered the portion present only in the long isoform. The prefix of gene_id should be an identifier for the gene and each identifier has to be associated with only one "_PRE" and one "_POST", leading to two genomic region associated to each gene_id.

Value

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

See Also

RoarDataset

Examples

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