VcfDB: Class '"VcfDB"'

In dbottomly/oligoMask: Tools for masking out problematic Affymetrix probes using VCF files and the oligo package

Description

A simple class representing an SQLite database representation of a VCF file for use with the oligoMask package

Objects from the Class

Objects can be created by calls of the form new("VcfDB", ...).

Slots

db.path:

Object of class "character" containing the file path to the database

tbsl:

Object of class "TableSchemaList" containing the schema of the database

start.var.table:

Object of class "character" when determining how to join the tables in order to perform the masking procedure, the table to start from.

end.var.table:

Object of class "character" when determining how to join the tables in order to perform the masking procedure, the table to end at.

var.mask.probe.id:

Object of class "character" column that the variant mask database uses to denote the probe ID

var.mask.var.id:

Object of class "character" column that the variant mask database uses to denote each variant

Methods

vcfDb

signature(obj = "VcfDB"): Returns the filename

tbsl

signature(obj = "VcfDB"): Returns the TableSchemaList object

Author(s)

Daniel Bottomly

See Also

TableSchemaList

Examples

temp.vcf.db <- new("VcfDB", db.path=om.db.file(), tbsl=SangerTableSchemaList())

vcfDb(temp.vcf.db)
tbsl(temp.vcf.db)

dbottomly/oligoMask documentation built on May 15, 2019, 1:22 a.m.