timepointDE: Differential timepoint expression testing.
In nlhuong/vistimeseq: Analysis for short time-series data

Description Usage Arguments Value Examples

View source: R/differential_expression.R

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

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

`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.

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

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