counts2lFC: Calculate log2FoldChange

In intePareto: Integrative Analysis of RNA-Seq and ChIP-Seq Data

Description

counts2lFC calculates log2FoldChange from counts.

Usage

counts2lFC(
  countData,
  colData,
  condition,
  ref,
  type = "apeglm",
  apeAdapt = FALSE,
  ...
)

Arguments

countData	a matrix of counts.
colData	a data.frame with at least a single column. Rows of colData correspond to columns of countData.
condition	the formula expresses how the counts for each gene depend on the variables in colData. The comparisons will be based on the alphabetical order of the levels by default. You can also specify the reference level by ref parameter
ref	specifying the reference level
type	shrinkage estimator, default is "apeglm", the adaptive t prior shrinkage estimator from the 'apeglm' package.
apeAdapt	logical, should apeglm use the MLE estimates of LFC to adapt the prior, or use default.
...	refer to DESeq2::lfcShrink() for more detailed parameters.

Value

resLFC a dataframe contains log2FoldChange.

# Please note this is a downsampling of the original data.

intePareto documentation built on June 18, 2021, 5:08 p.m.