runFullScan: runFullScan

In ETHZ-INS/scanMiRApp: scanMiR shiny application

runFullScan

Description

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

Usage

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

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

ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 p.m.