simulateRPF {ribosomeProfilingQC} | R Documentation |
Simulate the RPFs reads in CDS, 5'UTR and 3'UTR
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 )
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. |
An invisible list of GAlignments.
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)