yCrypticRNAs (version 0.99.2)

genome_wide_scores: Genome-wide cryptic scores.

Description

Genome-wide calculation of cryptic scores with a specified method.

Usage

genome_wide_scores(coverageDataSet, method = c("ratio", "enrichment", "probabilistic"), outfile, introns = NULL, windowLength = 100, iterations = 10000)

Arguments

coverageDataSet

A coverageDataSet containing the coverage values for all genes.

method

A caracter vector indicating the method to be used.

outfile

A character vector indicating the output file name.

introns

An objet of type annotationsSet containing the annotations of the intronic regions. Note: The introns must have same name as the gene they are associated with.

windowLength

If the method is "ratio", specify the length of the window to use at each end of the gene.

iterations

If the method is "probabilistic", specify the number of iterations.

Examples

data("rna_seq_signals")
#genome_wide_scores(rna_seq_signals, "ratio", "ratio.txt")
genome_wide_scores(rna_seq_signals, "enrichment", "enrichment.txt")
#genome_wide_scores(rna_seq_signals, "probabilistic", "probabilistic.txt")
unlink(c("ratio.txt", "enrichment.txt", "probabilistic.txt"))