log2FC: log2FC

In plger/sechm: sechm: Complex Heatmaps from a SummarizedExperiment

log2FC

Description

Generates log2(foldchange) matrix/assay, eventually on a per-batch fashion.

Usage

log2FC(
  x,
  fromAssay = NULL,
  controls,
  by = NULL,
  isLog = NULL,
  agFun = rowMeans,
  toAssay = "log2FC",
  pseudocount = 1L,
  ndigits = 2
)

Arguments

x	A numeric matrix, or a 'SummarizedExperiment' object
fromAssay	The assay to use if 'x' is a 'SummarizedExperiment'
controls	A vector of which samples should be used as controls for foldchange calculations.
by	An optional vector indicating groups/batches by which the controls will be averaged to calculate per-group foldchanges.
isLog	Logical; whether the data is log-transformed. If NULL, will attempt to figure it out from the data and/or assay name
agFun	Aggregation function for the baseline (default rowMeans)
toAssay	The name of the assay in which to save the output. If left to the default value, both a log2FC assay as well as a scaled log2FC assay (scaled by unit-variance, but not centered) will be saved in the object.
pseudocount	If the origin assay is not log-transformed, 'pseudocount' will be added to the values before calculating a log-transformation. This prevents infinite fold-changes and moderates them.
ndigits	Number of digits after the decimal of the log2FC (and scaledLFC).

Value

An object of same class as 'x'; if a 'SummarizedExperiment', will have the additional assay named from 'toAssay'.

Examples

log2FC( matrix(rnorm(40), ncol=4), controls=1:2 )

plger/sechm documentation built on Nov. 15, 2024, 5:08 a.m.