CompoundVariantSet: Create CompoundVariantSet from variant IDs

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Create CompoundVariantSet from variant IDs

Description

A CompoundVariantSet is a collection of "compound variants". A compound variant is an arbitrary group of variants that have sequencing coverage across some set of samples. (Any of these samples with one or more of the constituent SNVs "has the compound variant"–samples with coverage at only some of the sites are not considered.) The compound variants within a CompoundVariantSet are always disjoint: that is, no individual variant appears in more than one of the compound variants.

Usage

CompoundVariantSet(cesa, variant_id)

Arguments

cesa	CESAnalysis (used to access variant annotations)
variant_id	Vector of variant IDs to include in one compound variant, or a list of vectors, each of which defines a separate compound variant. If the vector or list is named, names will be kept. Otherwise, compound variants will be named sequentially.

Details

Example: CompoundVariantSet(cesa, variant_id = list(kras12 = c("KRAS G12C", "KRAS G12D", "KRAS G12V"))) creates a CompoundVariantSet containing one compound variant. To create a large set, it's usually easier to use define_compound_variants(), which calls this function internally to define compound variants from an input variant table.

If you're using this function because you have a complex use case that define_compound_variants() can't handle, please let us know so we can try to make improvements!

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.