FLOSS: Fragment Length Organization Similarity Score (FLOSS)

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Fragment Length Organization Similarity Score (FLOSS)

Description

The FLOSS will be calculated from a histogram of read lengths for footprints on a transcript or reading frame.

Usage

FLOSS(
  reads,
  ref,
  CDS,
  readLengths = c(26:34),
  level = c("tx", "gene"),
  draw = FALSE,
  ignore.seqlevelsStyle = FALSE
)

Arguments

reads	Output of getPsiteCoordinates
ref	Refercence id list. If level is set to tx, the id should be transcript names. If level is set to gene, the id should be gene id.
CDS	Output of prepareCDS
readLengths	Read length used for calculation
level	Transcript or gene level
draw	Plot FLOSS vs total reads or not.
ignore.seqlevelsStyle	Ignore the sequence name style detection or not.

Value

A data frame with colnames as id, FLOSS, totalReads, wilcox.test.pval, cook's distance.

References

1: Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 2014 Sep 11;8(5):1365-79. doi: 10.1016/j.celrep.2014.07.045. Epub 2014 Aug 21. PubMed PMID: 25159147; PubMed Central PMCID: PMC4216110.

Examples

library(Rsamtools)
bamfilename <- system.file("extdata", "RPF.WT.1.bam",
                           package="ribosomeProfilingQC")
yieldSize <- 10000000
bamfile <- BamFile(bamfilename, yieldSize = yieldSize)
pc <- getPsiteCoordinates(bamfile, bestpsite=13)
#library(GenomicFeatures)
library(BSgenome.Drerio.UCSC.danRer10)
#txdb <- makeTxDbFromGFF(system.file("extdata",
 #         "Danio_rerio.GRCz10.91.chr1.gtf.gz",
 #         package="ribosomeProfilingQC"),
 #         organism = "Danio rerio",
 #         chrominfo = seqinfo(Drerio)["chr1"],
 #         taxonomyId = 7955)
#CDS <- prepareCDS(txdb)
CDS <- readRDS(system.file("extdata", "CDS.rds",
                           package="ribosomeProfilingQC"))
set.seed(123)
ref <- sample(unique(CDS$gene_id), 100)
fl <- FLOSS(pc, ref, CDS, level="gene")

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