DEqual: Differential expression quality (DEqual) plot

In LieberInstitute/qsvaR: Generate Quality Surrogate Variable Analysis for Degradation Correction

Differential expression quality (DEqual) plot

Description

A DEqual plot compares the effect of RNA degradation from an independent degradation experiment on the y axis to the effect of the outcome of interest. They were orignally described by Jaffe et al, PNAS, 2017 https://doi.org/10.1073/pnas.1617384114. Other DEqual versions are included in Collado-Torres et al, Neuron, 2019 https://doi.org/10.1016/j.neuron.2019.05.013. This function compares your t-statistics of interest computed on transcripts against the t-statistics from degradation time adjusting for the six brain regions from degradation experiment data used for determining covComb_tx_deg.

Usage

DEqual(DE)

Arguments

DE	a data.frame() with one column containing the t-statistics from Differential Expression, typically generated with limma::topTable(). The rownames(DE) should be transcript GENCODE IDs.

Value

a ggplot object of the DE t-statistic vs the DE statistic from degradation

Examples

## Random differential expression t-statistics for the same transcripts
## we have degradation t-statistics for in `degradation_tstats`.
set.seed(101)
random_de <- data.frame(
    t = rt(nrow(degradation_tstats), 5),
    row.names = sample(
        rownames(degradation_tstats),
        nrow(degradation_tstats)
    )
)

## Create the DEqual plot
DEqual(random_de)

LieberInstitute/qsvaR documentation built on June 22, 2024, 8:03 a.m.