R: Perform 4sU dropout tests

dropout {grandR}

R Documentation

Perform 4sU dropout tests

Description

Testing for RNA dropout 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

Plot4sUDropoutRankAll(data, pairs = Findno4sUPairs(data), ...)

Plot4sUDropoutAll(data, pairs = Findno4sUPairs(data), ...)

Plot4sUDropoutDeferAll(data, pairs = NULL, ...)

Plot4sUDropoutRankDeferAll(data, pairs = NULL, ...)

Plot4sUDropoutRank(
  data,
  w4sU,
  no4sU = Findno4sUPairs(data)[[w4sU]],
  ntr = w4sU,
  ylim = NULL,
  LFC.fun = lfc::PsiLFC,
  slot = "count",
  correction = 1,
  label.corr = TRUE,
  return.corr = FALSE,
  boxplot.bins = 10,
  title = w4sU,
  size = 1.5,
  invert.ranks = FALSE
)

Plot4sUDropout(
  data,
  w4sU,
  no4sU = Findno4sUPairs(data)[[w4sU]],
  ntr = w4sU,
  ylim = NULL,
  LFC.fun = lfc::PsiLFC,
  slot = "count",
  hl.quantile = 0.8,
  hl = NULL,
  correction = 1,
  label.corr = FALSE,
  return.corr = FALSE,
  title = w4sU,
  size = 1.5,
  color.by.ntr = FALSE
)

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
`label.corr`	add statistics as subtitle
`return.corr`	instead of only the ggplot object, return a list with slots plot (what is normally returned) and label (the correlation statistics)
`boxplot.bins`	how many boxplots for `Plot4sUDropoutRank`
`title`	the main title for the plot
`size`	the point size
`invert.ranks`	if TRUE, left to right on the plot is largest NTR to smallest NTR
`hl.quantile`	the half-life quantile to cut the plot
`hl`	if NULL, compute half-lives from the ntr column; otherwise, must be a vector containing half-lives
`color.by.ntr`	if true, compute the density colors along the ntr axis instead of globally

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.

Value