annotate_variants: Annotate Variants

In andygxzeng/ECSI: Espresso - Somatic Mutation Calling using Contextual Error Models

Description

Wrapper function for variant annotation from CellBase through cellbaseR Returns a dataframe with mutations annotated by CellBase - requires internet connection.

Usage

annotate_variants(variant_calls, genome = c("hg19", "hg38"), batchsize = 80)

Arguments

variant_calls	VRanges object from call_all_variants output
genome	Genome of input object, accepts either hg19 or hg38
batchsize	Size of variant batches to send to CellBase - the API will time out if processing >100 variants at a time. If it does time out, reduce the batchsize.

Value

This function returns a DataFrame object with annotations for each variant.

Examples

## Not run: 
annotated_variants <- annotate_variants(variant_calls, genome="hg19")

## End(Not run)

andygxzeng/ECSI documentation built on Feb. 6, 2021, 8:53 a.m.