simulateRPF: Simulation function

In jianhong/ribosomeProfilingQC: Ribosome Profiling Quality Control

Simulation function

Description

Simulate the RPFs reads in CDS, 5'UTR and 3'UTR

Usage

simulateRPF(
  txdb,
  outPath,
  genome,
  samples = 6,
  group1 = c(1, 2, 3),
  group2 = c(4, 5, 6),
  readsPerSample = 1e+06,
  readsLen = 28,
  psite = 13,
  frame0 = 0.9,
  frame1 = 0.05,
  frame2 = 0.05,
  DEregions = GRanges(),
  size = 1,
  sd = 0.02,
  minDElevel = log2(2),
  includeReadsSeq = FALSE
)

Arguments

txdb	A TxDb object
outPath	Output folder for the bam files
genome	A BSgenome object
samples	Total samples to simulate.
group1, group2	Numeric to index the sample groups.
readsPerSample	Total reads number per sample.
readsLen	Reads length, default 100bp.
psite	P-site position. default 13.
frame0, frame1, frame2	Percentage of reads distribution in frame0, frame1 and frame2
DEregions	The regions with differential reads in exon, utr5 and utr3.
size	Dispersion parameter. Must be strictly positive.
sd	Standard deviations.
minDElevel	Minimal differential level. default: log2(2).
includeReadsSeq	logical(1). Include reads sequence or not.

Value

An invisible list of GAlignments.

Examples

library(GenomicFeatures)
txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)
simulateRPF(txdb, samples=1, readsPerSample = 1e3)
## Not run: 
cds <- prepareCDS(txdb, withUTR = TRUE)
cds <- cds[width(cds)>200]
DEregions <- cds[sample(seq_along(cds), 10)]
simulateRPF(txdb, samples=6, readsPerSample = 1e5, DEregions=DEregions)

## End(Not run)

jianhong/ribosomeProfilingQC documentation built on April 15, 2024, 7:10 p.m.