runFullScan {scanMiRApp} | R Documentation |
Runs a full miRNA scan on all protein-coding transcripts (or UTRs) of an annotation.
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, ... )
annotation |
A |
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 |
shadow |
The size of the ribosomal shadow at the UTR starts |
cores |
The number of threads to use. Alternatively accepts a
|
maxLogKd |
The maximum log_kd of sites to report |
save.path |
Optional, the path to which to save the results |
... |
Arguments passed to |
A 'GRanges' object
anno <- ScanMiRAnno("fake") m <- runFullScan( annotation=anno ) m