entropy {ORFik} | R Documentation

## Calucalte entropy value of overlapping input reads per GRanges.

### Description

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.

### Usage

    entropy(grl, reads)

### Arguments

`grl` | a `GRangesList` that the reads will be overlapped with
`reads` | a GAlignment object or GRanges or GRangesList, usualy data from RiboSeq or RnaSeq

### Value

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

### See Also

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`

### Examples

    # 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)

[Package ORFik version 1.4.1 Index]