coverageDataSet: Create a CoverageDataSet
In yCrypticRNAs: Cryptic Transcription Analysis in Yeast

Description Usage Arguments Value Examples

Create a CoverageDataSet containing the depth and breadth of coverage of genes in annotations.

1 2	coverageDataSet(bamfiles, annotations, types, sf = c(1, 1, 1, 1), paired_end = TRUE, as_fragments = TRUE)

`bamfiles`	A vector of characters indicating the BAM files paths.
`annotations`	An object of type `annotationsSet` containing information on genes.
`types`	A vector of the same length as `bamfiles` indicating the type of data in each file. Example: WT vs MUT or untreated vs treated".
`sf`	A vector of the same length as `bamfiles` indicating the scaling factor to apply on each file. Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM).
`paired_end`	logical indicating whether the `bamfiles` contains paired-end data.
`as_fragments`	logical indicating if paired-end data must paired and merged to form fragments.

An object of class 'coverageDataSet' containing the coverage for each sample. The details of the output componets are as follow:

data

A data.table with the following components:

chrom: Gene chromosome.
start: Gene transcription start site.
end: Gene transcription termination site.
name: Gene name.
score: Gene score.
strand: Gene strand.
pos: One based positions of the gene.
...: For each sample, report the depth at each position of the gene per sample.

samples

A list containg the samples' names that are in the coverageDataSet.

type1: Type1 samples names (controls)
type2: Type2 samples names (experiment)

samples <- c("wt_rep1", "wt_rep2", "mut_rep1", "mut_rep2")
bamfiles <- system.file("extdata", paste0(samples, ".bam"),
                              package = "yCrypticRNAs")
data(annotations)
types <- c("wt", "wt", "mut", "mut")
scaling_factors <- c(0.069872847, 0.081113079, 0.088520251, 0.069911116)
rna_seq_signals <- coverageDataSet (bamfiles, annotations, types, scaling_factors)
rna_seq_signals