timepointDE: Differential timepoint expression testing.

In nlhuong/TimeSeriesExperiment: Analysis for short time-series data

Description

This is a wrapper around lmFit and voom functions from limma package for testing differential expression at specified timepoints.

Usage

timepointDE(object, timepoints = "all", min_gene_sum = 1, alpha = 0.05)

Arguments

object	A TimeSeriesExperiment object.
timepoints	Vector of timepoints to test at.
min_gene_sum	A scalar for filtering sparse genes before DE testing. Default is 1.
alpha	A scalar for level of significance. Default is 0.05.

Value

a TimeSeriesExperiment object with timepoint differential expression testing results stored in 'timepoint_de' element in diff.expr slot.

Examples

data("endoderm_small")
endoderm_small <- timepointDE(endoderm_small, timepoint = 1.0)
head(differentialExpression(endoderm_small, "timepoint_de")$`1`)

nlhuong/TimeSeriesExperiment documentation built on Sept. 8, 2021, 12:30 a.m.