entropy: Percentage of maximum entropy
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

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.

1	entropy(grl, reads, weight = 1L, is.sorted = FALSE, overlapGrl = NULL)

`grl`	a `GRangesList` object can be either transcripts, 5' utrs, cds', 3' utrs or ORFs as a special case (uORFs, potential new cds' etc). If regions are not spliced you can send a `GRanges` object.
`reads`	a `GAlignments`, `GRanges` or `GRangesList` object, usually of RiboSeq, RnaSeq, CageSeq, etc.
`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.
`is.sorted`	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`overlapGrl`	an integer, (default: NULL), if defined must be countOverlaps(grl, RFP), added for speed if you already have it

A numeric vector containing one entropy value per element in 'grl'

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