Nothing
## ------------------------------------------------------------------------
library(denovolyzeR)
# have a look at the example data:
dim(autismDeNovos)
head(autismDeNovos)
## ------------------------------------------------------------------------
denovolyzeByClass(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078)
## ------------------------------------------------------------------------
denovolyzeMultiHits(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078)
## ------------------------------------------------------------------------
denovolyzeMultiHits(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078,
nperms=1000)
## ------------------------------------------------------------------------
sum(autismDeNovos$class %in% c("frameshift","non","splice"))
## ------------------------------------------------------------------------
denovolyzeMultiHits(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078,
nperms=1000,
nVars="expected")
## ------------------------------------------------------------------------
head(
denovolyzeByGene(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078)
)
## ----geneset-------------------------------------------------------------
nrow(fmrpGenes); head(fmrpGenes)
denovolyzeByClass(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078,
includeGenes=fmrpGenes$geneName)
denovolyzeMultiHits(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078,
nperms=1000,
includeGenes=fmrpGenes$geneName)
## ----viewProbabilityTable------------------------------------------------
head(
viewProbabilityTable()
)
head(
viewProbabilityTable(format="long")
)
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