simulate_experiment_empirical {polyester} | R Documentation |
Create fasta files representing reads from a two-group experiment, where abundances and differential expression are estimated from a real data set
simulate_experiment_empirical( bg = NULL, fpkmMat = NULL, mean_rps = 5e+06, grouplabels = NULL, decut = 1.5, outdir = ".", ... )
bg |
Ballgown object containing estimated transcript abundances in FPKM.
Reads will be simulated for the same number of replicates that are in
|
fpkmMat |
transcript-by-sample matrix containing abundances (in FPKM) estimated from a real data set. MUST have row names identifying transcripts. The number of columns is the number of samples that will be simulated. |
mean_rps |
Number of reads per sample to use in converting FPKM measurements to counts. Should be somewhat close to the number of reads per sample in the experiment that generated the estimated FPKMs. Defaults to 5 million (5e6). |
grouplabels |
vector indicating the group labels for each replicate in the experiment. Must be convertible to a factor with exactly 2 levels. |
decut |
A transcript will be recorded as truly differentially expressed
if its fold change between the two groups is more extreme than
|
outdir |
character, path to folder where simulated reads should be written, without a slash at the end of the folder name. By default, reads written to the working directory. |
... |
Additional arguments to pass to simulate_experiment_countmat |
No return, but reads are written to outdir
.
## Not run: library(ballgown) data(bg) bg = subset(bg, "chr=='22'") # load gtf file: gtfpath = system.file('extdata', 'bg.gtf.gz', package='polyester') gtf = subset(gffRead(gtfpath), seqname=='22') # load/download chromosome sequence (just for this example) system('wget https://www.dropbox.com/s/04i6msi9vu2snif/chr22seq.rda') load('chr22seq.rda') names(chr22seq) = '22' # simulate reads based on this experiment's FPKMs simulate_experiment_empirical(bg, grouplabels=pData(bg)$group, gtf=gtf, seqpath=chr22seq, mean_rps=5000, outdir='simulated_reads_3', seed=1247) ## End(Not run)