genome_wide_scores: Genome-wide cryptic scores.
In yCrypticRNAs: Cryptic Transcription Analysis in Yeast

View source: R/cryptic_transcripts_methods.R

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

1
2
3

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

`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.

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"))