FLOSS {ribosomeProfilingQC} | R Documentation |
The FLOSS will be calculated from a histogram of read lengths for footprints on a transcript or reading frame.
FLOSS( reads, ref, CDS, readLengths = c(26:34), level = c("tx", "gene"), draw = FALSE )
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. |
A data frame with colnames as id, FLOSS, totalReads, wilcox.test.pval, cook's distance.
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.
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")