testCoefficient: Calculate the significance of a factor in the regression...

In YosefLab/MPRAnalyze: Statistical Analysis of MPRA data

Description

Calculate the significance of a factor in the regression model

Usage

testCoefficient(obj, factor, contrast)

Arguments

obj	the MpraObject
factor	the name of the factor to make the comparison on
contrast	the character value of the factor to use as a contrast. See details.

Value

a data.frame of the results this include the test statistic, logFC, p-value and BH-corrected FDR.

Examples

data <- simulateMPRA(tr = rep(2,5), da=c(rep(0,2), rep(1,3)), 
                     nbatch=2, nbc=15)
obj <- MpraObject(dnaCounts = data$obs.dna, 
                  rnaCounts = data$obs.rna, 
                  colAnnot = data$annot)
obj <- estimateDepthFactors(obj, lib.factor = "batch", which.lib = "both")

## fit.se must be TRUE for coefficient based testing to work
obj <- analyzeComparative(obj, dnaDesign = ~ batch + barcode + condition, 
                              rnaDesign = ~ condition, fit.se = TRUE)
results <- testCoefficient(obj, "condition", "contrast")

YosefLab/MPRAnalyze documentation built on Nov. 14, 2020, 2:35 a.m.