riboTISCoverageProportion {ORFik} | R Documentation |
Proportion defined as: average count per position in -20,20 normalized by counts per gene
riboTISCoverageProportion(grl, tx, footprints, onlyProportion = FALSE, average = FALSE, pShifted = TRUE, keep.names = FALSE, upStart = if (pShifted) 5 else 20, downStop = if (pShifted) 20 else 5)
grl |
a |
tx |
a GrangesList of transcripts covering grl. |
footprints |
ribo seq reads as GAlignment, GRanges or GRangesList object. |
onlyProportion |
a logical (FALSE), return whole data.frame or only proportions |
average |
a logical (FALSE), take average over coverage in all grl ? |
pShifted |
a logical (TRUE), are riboseq reads p-shifted? |
keep.names |
a logical(FALSE), only applies when onlyProportion is TRUE. |
upStart |
upstream region boundary (5 or 20 as standard), relative (5, mean 5 upstream from TIS) |
downStop |
downstream region boundary (5 or 20 as standard), relative (5, mean 5 downstream from TIS) |
This pattern can be averaged on CDS's, to find other ORFs. When detecting new ORFs, this CDS average can be used as a template.
a data.frame with lengths by coverage / vector of proportions