QueryBuilder: Construct a QueryBuilder object given a compilation and one...

In langmead-lab/snapcount: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

Construct a QueryBuilder object given a compilation and one or regions.

Description

Construct a QueryBuilder object given a compilation and one or regions.

Usage

QueryBuilder(compilation, regions)

Arguments

compilation	A single string containing the name of the Snaptron data source. Any variant of the Compilation enum can also be passed an argument.
regions	Either a list of 1 more HUGO gene names as strings e.g. "BRCA1" or a Granges class object containing one or more geneomic intervals (e.g. "chr1:1-1000").

Value

A QueryBuilder object.

Examples

# contruct a query builder for GTEX data source and BRAC1 gene
qb <- QueryBuilder(compilation = Compilation$gtex, regions = "BRCA1")

# contruct a query builder for TCGA data source and chromosome region
qb <- QueryBuilder(compilation = "tcga", regions = "chr1:1-1000")

# construct a query builder for TCGA data source using GRanges object
library(GenomicRanges)
qb <- QueryBuilder(compilation = "tcga", regions = GRanges("chr1", "1-1000"))

langmead-lab/snapcount documentation built on May 1, 2022, 4:27 a.m.