startRegionCoverage: Start region coverage

In Roleren/ORFik: Open Reading Frames in Genomics

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 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: 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)

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.