Basic data elements required for the HMM

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(oligoClasses)
Welcome to oligoClasses version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligoClasses/locusLevelData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: locusLevelData
> ### Title: Basic data elements required for the HMM
> ### Aliases: locusLevelData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(locusLevelData)
> str(locusLevelData)
List of 5
 $ annotation     : chr [1:9265, 1:2] "1" "1" "1" "1" ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:9265] "SNP_A-1677174" "SNP_A-1718890" "SNP_A-1678466" "SNP_A-1676440" ...
  .. ..$ : chr [1:2] "chromosome" "position"
 $ copynumber     : int [1:9265, 1] 200 171 120 112 142 97 217 176 260 164 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:9265] "SNP_A-1677174" "SNP_A-1718890" "SNP_A-1678466" "SNP_A-1676440" ...
  .. ..$ : chr "NA06993"
 $ genotypes      : num [1:9265, 1] 1 1 2 1 1 2 2 1 1 2 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:9265] "SNP_A-1677174" "SNP_A-1718890" "SNP_A-1678466" "SNP_A-1676440" ...
  .. ..$ : chr "NA06993"
 $ crlmmConfidence: num [1:9265, 1] 7206 5949 6680 6690 7026 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:9265] "SNP_A-1677174" "SNP_A-1718890" "SNP_A-1678466" "SNP_A-1676440" ...
  .. ..$ : chr "NA06993"
 $ platform       : chr "pd.mapping50k.hind240,pd.mapping50k.xba240"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>