doIntegration: Do integrative analysis

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

Description

doIntegration calculate log2FoldChange of RNA-Seq and ChIP-Seq and then calculate Z scores for each marker.

Usage

doIntegration(res, ref, type = "apeglm", apeAdapt = FALSE)

Arguments

res	a list result from doMatch function.
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.

Value

df_final a dataframe contains log2FoldChange of RNA-Seq and ChIP-Seq and Z scores for each marker.

Examples

data(res)
doIntegration(res = res,ref="wild.type")

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