getORFscore: Calculate ORFscore

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Calculate ORFscore

Description

To calculate the ORFscore, reads were counnted at each position within the ORF.

ORFscore = log_2((\sum_{n=1}^{3}\frac{(F_i-\bar{F})^2}{\bar{F}}) + 1)

where F_n is the number of reads in reading frame n, \bar{F} is the total number of reads across all three frames divided by 3. If F_1 is smaller than F_2 or F_3, ORFscore = -1 X ORFscore.

Usage

getORFscore(reads)

Arguments

reads

Output of getPsiteCoordinates

Value

A numeric vector with ORFscore.

References

1: Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4. PubMed PMID: 24705786; PubMed Central PMCID: PMC4193932.

Examples

pcs <- readRDS(system.file("extdata", "samplePc.rds",
               package="ribosomeProfilingQC"))
ORFscore <- getORFscore(pcs)

jianhong/ribosomeProfilingQC documentation built on Nov. 3, 2024, 6:33 p.m.