| entropy {ORFik} | R Documentation |
Calculates entropy of the 'reads' coverage over each 'grl' group. The entropy value per group is a real number in the interval (0:1), where 0 indicates no variance in reads over group. For example c(0,0,0,0) has 0 entropy, since no reads overlap.
entropy(grl, reads)
grl |
a |
reads |
a GAlignment object or GRanges or GRangesList, usualy data from RiboSeq or RnaSeq |
A numeric vector containing one entropy value per element in 'grl'
Other features: computeFeaturesCage,
computeFeatures,
disengagementScore,
distToCds, floss,
fpkm_calc, fpkm,
fractionLength,
insideOutsideORF, isInFrame,
isOverlapping,
kozakSequenceScore, orfScore,
rankOrder,
ribosomeReleaseScore,
ribosomeStallingScore,
subsetCoverage,
translationalEff
ORF <- GRanges("1", ranges = IRanges(start = c(1, 12, 22),
end = c(10, 20, 32)),
strand = "+",
names = rep("tx1_1", 3))
names(ORF) <- rep("tx1", 3)
grl <- GRangesList(tx1_1 = ORF)
RFP <- GRanges("1", IRanges(c(25, 35), c(25, 35)), "+")
# grl must have same names as cds + _1 etc, so that they can be matched.
entropy(grl, RFP)
# or on cds
cdsORF <- GRanges("1", IRanges(35, 44), "+", names = "tx1")
names(cdsORF) <- "tx1"
cds <- GRangesList(tx1 = cdsORF)
entropy(cds, RFP)