startRegionCoverage {ORFik} | R Documentation |
Get the number of reads in the start region of each ORF. If you want the start codon coverage only, set upstream = 0. Standard is 2 upstream and 2 downstream, a width 5 window centered at start site. since p-shifting is not 100 start site.
startRegionCoverage(grl, RFP, tx = NULL, is.sorted = TRUE, upstream = 2L, downstream = 2L)
grl |
a |
RFP |
ribo seq reads as GAlignment, GRanges or GRangesList object |
tx |
default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id" |
is.sorted |
logical (TRUE), is grl sorted. |
upstream |
an integer (2), relative region to get upstream from. |
downstream |
an integer (2), relative region to get downstream from |
If tx is null, then upstream will be force to 0 and downstream to a maximum of grl width. Since there is no reference for splicing.
a numeric vector of counts
Other features: computeFeaturesCage
,
computeFeatures
,
disengagementScore
,
distToCds
, distToTSS
,
entropy
, floss
,
fpkm_calc
, fpkm
,
fractionLength
,
initiationScore
,
insideOutsideORF
, isInFrame
,
isOverlapping
,
kozakSequenceScore
, orfScore
,
rankOrder
,
ribosomeReleaseScore
,
ribosomeStallingScore
,
startRegion
, subsetCoverage
,
translationalEff