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
, distToTSS
,
floss
, fpkm_calc
,
fpkm
, fractionLength
,
initiationScore
,
insideOutsideORF
, isInFrame
,
isOverlapping
,
kozakSequenceScore
, orfScore
,
rankOrder
,
ribosomeReleaseScore
,
ribosomeStallingScore
,
startRegionCoverage
,
startRegion
, subsetCoverage
,
translationalEff
# a toy example with ribo-seq p-shifted reads 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) reads <- 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, reads) # or on cds cdsORF <- GRanges("1", IRanges(35, 44), "+", names = "tx1") names(cdsORF) <- "tx1" cds <- GRangesList(tx1 = cdsORF) entropy(cds, reads)