runFullScan: runFullScan

Description Usage Arguments Value Examples

View source: R/runFullScan.R

Description

Runs a full miRNA scan on all protein-coding transcripts (or UTRs) of an annotation.

Usage

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runFullScan(
  annotation,
  mods = NULL,
  annoFilter = NULL,
  extract = c("UTRonly", "withORF", "exons"),
  onlyCanonical = TRUE,
  shadow = 15,
  cores = 1,
  maxLogKd = c(-1, -1.5),
  save.path = NULL,
  ...
)

Arguments

annotation

A ScanMiRAnno object

mods

An optional 'KdModelList' (defaults to the one in 'annotation')

annoFilter

An optional 'AnnotationFilter' or 'AnnotationFilterList' to filter the set of transcripts to be extracted

extract

Which parts of the transcripts to extract. For 'UTRonly' (default) only the 3' UTR regions are extracted, 'withORF' additionally extracts the coding regions, and 'exons' extracts all exons

onlyCanonical

passed to findSeedMatches

shadow

The size of the ribosomal shadow at the UTR starts

cores

The number of threads to use. Alternatively accepts a BiocParallelParam-class, as for instance produced by MulticoreParam.

maxLogKd

The maximum log_kd of sites to report

save.path

Optional, the path to which to save the results

...

Arguments passed to findSeedMatches

Value

A 'GRanges' object

Examples

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anno <- ScanMiRAnno("fake")
m <- runFullScan( annotation=anno )
m

ETHZ-INS/scanMiRApp documentation built on Jan. 20, 2022, 5:51 p.m.