entropy: Percentage of maximum entropy

In JokingHero/ORFik: Open Reading Frames in Genomics

Percentage of maximum entropy

Description

Calculates percentage of maximum entropy of the 'reads' coverage over each ORF in 'grl' group. The entropy value per group is a real number in the interval (0:1), where 0 indicates no variance in reads over all codons of group For example c(0,0,0,0) has 0 entropy, since no reads overlap.
Interval: [0]: No reads or all reads in 1 place
Interval: [0.01-0.99]: >= 2 positions covered
Interval: [1]: all positions covered perfectly in frame

Usage

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

Arguments

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 numeric/integer vector or metacolumn name. (default: 1L, no differential weighting). If weight is name of defined meta column in reads object, it gives the number of times a read was found at that position. GRanges("chr1", 1, "+", score = 5), would mean "score" column tells that this alignment region was found 5 times. if 1L it means each read is weighted equal as 1, this is what among others countOverlaps() presumes, if single number (!= 1), it repeats for all ranges, if vector with length > 1, it must be equal size of the reads object.
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.

Value

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

See Also

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

Examples

# a toy example with ribo-seq p-shifted reads
ORF <- GRangesList(tx1 = GRanges("1", IRanges(1, width = 9), "+"))
entropy(ORF, GRanges()) # 0
entropy(ORF, GRanges("1", IRanges(c(1)), "+")) # 0
entropy(ORF, GRanges("1", IRanges(c(1,4,6,7)), "+")) # 0.94
entropy(ORF, GRanges("1", IRanges(c(1,4,7)), "+", score = c(1,2,1)),
        weight = "score") # 0.94
entropy(ORF, GRanges("1", IRanges(c(1,4,7)), "+")) # Perfect = 1

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.