locusLevelData: Basic data elements required for the HMM

In oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

This object is a list containing the basic data elements required for the HMM

Usage

data(locusLevelData)

Format

A list

Details

The basic assay data elements that can be used for fitting the HMM are:

1. a mapping of platform identifiers to chromosome and physical position

2. (optional) a matrix of copy number estimates

3. (optional) a matrix of confidence scores for the copy number estimates (e.g., inverse standard deviations)

4. (optional) a matrix of genotype calls

5. (optional) CRLMM confidence scores for the genotype calls

At least (2) or (4) is required. The locusLevelData is a list that contains (1), (2), (4), and (5).

Source

A HapMap sample on the Affymetrix 50k platform. Chromosomal alterations were simulated. The last 100 SNPs on chromosome 2 are, in fact, a repeat of the first 100 SNPs on chromosome 1 – this was added for internal use.

Examples

data(locusLevelData)
str(locusLevelData)

oligoClasses documentation built on Nov. 8, 2020, 5:32 p.m.