startRegionCoverage: Start region coverage

startRegionCoverageR Documentation

Start region coverage

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 numeric/integer vector or metacolumn name. (default: 1L, no differential weighting). If weight is name of defined meta column in reads object, it gives the number of times a read was found at that position. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times. if 1L it means each read is weighted equal as 1, this is what among others countOverlaps() presumes, if single number (!= 1), it repeats for all ranges, if vector with length > 1, it must be equal size of the reads object.

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

Examples

ORF <- GRanges(seqnames = "1",
               ranges = IRanges(21, 40),
               strand = "+")
names(ORF) <- c("tx1")
grl <- GRangesList(tx1 = ORF)
tx <- extendLeaders(grl, 20)
# 1 width p-shifted reads
reads <- GRanges("1", IRanges(c(21, 23, 50, 50, 50, 53, 53, 56, 59),
                            width = 1), "+")
score(reads) <- 28 # original width
startRegionCoverage(grl, reads, tx)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.