Usage Arguments Author(s) Examples
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thresholdDetection |
minimum count per gene/sample. Default value = 1. |
fractionExpressed |
fraction of samples expressed (above thresholdDetection). Default value = .01. |
Chiaowen Joyce Hsiao
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ipsc_eset <- get(load(system.file("testdata", "HumanTungiPSC.rda", package = "ashbun")))
counts <- exprs(ipsc_eset)[sample(nrow(exprs(ipsc_eset)), ), ]
#---- generat simulated datasets
library(ashbun)
simdata_list <- simulationWrapper(counts, Nsim = 2,
Ngenes = 100,
Nsam = 20,
sample_method = "all_genes",
pi0 = .5,
beta_args = args.big_normal(betapi = 1,
betamu = 0, betasd = .8))
#---- extract a single dataset as an example
#---- take pi0 = .9, the first simulated data
simdata <- simdata_list[[1]]
# ---- gather evaluation results
eval_ouptut <- query.evaluation(counts = simdata$counts,
condition = simdata$condition,
is_nullgene = simdata$is_nullgene,
methodsNormalize = c("TMM", "RLE"),
methodsMeanExpression = c("DESeq2", "limmaVoom"),
report = "fdr_cutoff_summary")
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