startRegionCoverage: Start region coverage

In ORFik: Open Reading Frames in Genomics

Description

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.

Usage

startRegionCoverage(
  grl,
  RFP,
  tx = NULL,
  is.sorted = TRUE,
  upstream = 2L,
  downstream = 2L,
  weight = 1L
)

Arguments

grl	a GRangesList object with usually either leaders, cds', 3' utrs or ORFs
RFP	ribo seq reads as GAlignments, 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
weight	a vector (default: 1L, if 1L it is identical to countOverlaps()), if single number (!= 1), it applies for all, if more than one must be equal size of 'reads'. else it must be the string name of a defined meta column in subject "reads", that gives number of times a read was found. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times.

Details

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.

Value

a numeric vector of counts

See Also

Other features: computeFeaturesCage(), computeFeatures(), countOverlapsW(), disengagementScore(), distToCds(), distToTSS(), entropy(), floss(), fpkm_calc(), fpkm(), fractionLength(), initiationScore(), insideOutsideORF(), isInFrame(), isOverlapping(), kozakSequenceScore(), orfScore(), rankOrder(), ribosomeReleaseScore(), ribosomeStallingScore(), startRegion(), stopRegion(), subsetCoverage(), translationalEff()

ORFik documentation built on March 27, 2021, 6 p.m.