permTestGeometricMean {transite} | R Documentation |
permTestGeometricMean
returns an estimate of the significance
of the observed
mean, given a set of random permutations of the data.
permTestGeometricMean(actual.mean, motif.kmers, random.permutations, alternative = c("two.sided", "less", "greater"), conf.level = 0.95, produce.plot = TRUE)
actual.mean |
observed mean |
motif.kmers |
set of k-mers that were used to compute
the |
random.permutations |
a set of random permutations of the original data, used to generate an empirical null distribution. |
alternative |
side of the test, one of the following:
|
conf.level |
confidence level for the returned confidence interval. |
produce.plot |
if distribution plot should be part of the returned list |
A list with the following components:
p.value.estimate | the estimated p-value of the observed mean |
conf.int | the confidence interval around that estimate |
plot | plot of the empirical distribution of geometric means of the enrichment values |
Other k-mer functions: calculateKmerEnrichment
,
checkKmers
,
computeKmerEnrichment
,
drawVolcanoPlot
,
empiricalEnrichmentMeanCDF
,
generateKmers
,
generatePermutedEnrichments
,
homopolymerCorrection
,
runKmerSPMA
, runKmerTSMA