entropy: Percentage of maximum entropy

In Roleren/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 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

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

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.