Testing for toxicity of a 4sU sample is performed by comparing half-lives or NTR ranks against the log2 fold change of the 4sU sample vs equivalent no4sU samples.
Usage
PlotToxicityTestRankAll(data, pairs = Findno4sUPairs(data), ...)
PlotToxicityTestAll(data, pairs = Findno4sUPairs(data), ...)
PlotToxicityTestDeferAll(data, pairs = NULL, ...)
PlotToxicityTestRankDeferAll(data, pairs = NULL, ...)
PlotToxicityTestRank(
data,
w4sU,
no4sU = Findno4sUPairs(data)[[w4sU]],
ntr = w4sU,
ylim = NULL,
LFC.fun = lfc::PsiLFC,
slot = "count",
correction = 1
)
PlotToxicityTest(
data,
w4sU,
no4sU = Findno4sUPairs(data)[[w4sU]],
ntr = w4sU,
ylim = NULL,
LFC.fun = lfc::PsiLFC,
slot = "count",
hl.quantile = 0.8,
correction = 1
)Arguments
- data
a grandR object
- pairs
a no4sU pairs list as generated by Findno4sUPairs
- ...
further arguments to be passed to or from other methods.
- w4sU
the name of a 4sU sample
- no4sU
the name(s) of equivalent no4sU sample(s)
- ntr
the name of a sample to take NTRs from (usually equal to w4sU)
- ylim
y axis limits
- LFC.fun
function to compute log fold change (default: PsiLFC, other viable option: NormLFC)
- slot
the slot of the grandR object to take the data from; for PsiLFC, this really should be "count"!
- correction
correction factor
- hl.quantile
the half-life quantile to cut the plot
Value
either a ggplot object, a list of ggplot objects, or a list of deferred functions for plotting
Details
The deferred versions are useful to be used in conjunction with ServeGrandR plot.static. Their implementation make sure that they are lightweight, i.e. when saving the returned function to an Rdata file, the grandR object is not stored.