DBscore: Differential binding analysis

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Differential binding analysis

Description

Use limma to do differential binding analysis for binding scores.

Usage

DBscore(se, design, coef, ...)

Arguments

se	An RangedSummarizedExperiment object. Outputs of getWeightedBindingScore.
design	Design table for lmFit.
coef	column number or column name specifying which coefficient or contrast of the linear model is of interest. See topTable.
...	Parameters can be used by lmFit.

Value

A RangedSummarizedExperiment object with the dataframe returned by topTable as appendence of the origin rowData.

Author(s)

Jianhong Ou

Examples

library(SummarizedExperiment)
set.seed(1)
sigma2 <- 0.05 / rchisq(100, df=10) * 10
y <- matrix(rnorm(100*6,sd=sqrt(sigma2)),100,6)
design <- cbind(Intercept=1,Group=c(0,0,0,1,1,1))
y[1,4:6] <- y[1,4:6] + 1
se <- SummarizedExperiment(assays=list(counts=y))
DBscore(se, design, coef=1)

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.