DE_data: Creates a 'DE_data' object

In hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results

Creates a DE_data object

Description

Creates a DE_data object from a tibble or data-frame of differential expression results.

Usage

DE_data(dat, keep_rownames_as = NULL)

Arguments

dat	Tibble, results from a differential expression analysis. See Details.
keep_rownames_as	Character, the name of the column in which to save the rownames of the input data-frame. Default value is NULL, i.e. rownames will be discarded.

Details

The input data should have one row per gene or transcript, and at least the following columns:

• chromosome: character column, chromosome on which the gene/transcript is located.

• start and end: numeric, starting and end position of the gene/transcript (in bp). A column position will be constructed as the middle value (mean) between start and end.

• score or padj: numeric, the DE score or adjusted p-value of the gene/transcript. If column score column is missing, will be constructed as -log10(padj).

• foldChange or log2FoldChange: numeric, the fold-change or log2(fold-change) of the gene/transcript. If column log2FoldChange is missing, will be constructed as log2(foldChange).

Value

A DE_data object, i.e. a tibble.

Examples

x <- get_example_data()

DE_data(x[["DE"]])

hidecan documentation built on Feb. 16, 2023, 6:22 p.m.