This directory contains some files describing the HVG detection machinery in scran.
In theory/
:
description.tex
focuses on the theoretical basis behindtrendVar
anddecomposeVar
.comparison.tex
considers the differences between the possible HVG detection methods in scran.
In real/
:
fitTrendVar_test.Rmd
tests the behaviour of thefitTrendVar()
on a range of scenarios.fitTrendCV2_test.Rmd
tests the behaviour of thefitTrendCV2()
on a range of scenarios.
In simulations/
:
power
contains simulation scripts to compare the performance ofdecomposeVar
withtechnicalCV2
andimprovedCV2
for detecting HVGs. Each simulation script describes a different type of variability, though this is not particularly important for gene-wise testing.alpha
assesses the type I error rate for the tests indecomposeVar
,technicalCV2
andimprovedCV2
.filter
examines the motivation for the default filter threshold intrendVar
.