check_sedesign: Check SEDesign object

In jmw86069/jamses: Jam SummarizedExperiment Stats

Check SEDesign object

Description

Check whether a SEDesign object is valid

Usage

check_sedesign(object)

Arguments

object

SEDesign object

Details

This function checks whether an SEDesign object is valid:

• if samples is provided, and if design is provided, samples must match rownames(design).

• if design is provided, and if contrasts is provided, colnames(design) must match rownames(contrasts).

• if contrasts is provided, design must also be provided.

Note that samples can be a subset of rownames(design), in which case the design will also be subset accordingly.

Similarly, colnames(design) can be a subset of rownames(contrasts), which would force contrasts to be subset accordingly.

Typically the order of samples should match the order of rownames(design) but this is not required. Downstream methods should confirm this order.

Typically the order of colnames(design) should match the order of rownames(contrast) but this is not required. Downstream methods should confirm this order.

See Also

Other jam experiment design: contrast2comp(), contrast_colors_by_group(), contrast_names_to_sedesign(), contrasts_to_factors(), contrasts_to_venn_setlists(), draw_oneway_contrast(), draw_twoway_contrast(), filter_contrast_names(), groups_to_sedesign(), plot_sedesign(), sedesign_to_factors(), validate_sedesign()

jmw86069/jamses documentation built on Nov. 4, 2024, 9:25 p.m.