prepdata: Prepares data for use with 'snpmclust'

Description Usage Arguments Details Value Author(s) References Examples

Description

Converts and transforms data from GenomeStudio output into form that can be handled by the function snpmclust.

Usage

1
prepdata(rawdata)

Arguments

rawdata

Data frame taken from an import of GenomeStudio full data table.

Details

prepdata expects a data frame that includes columns from an import of a GenomeStudio full data table. These columns include Name (the column of SNP rs-numbers) and the subcolumns Theta, R, GType, Score, X, Y, X.Raw, Y.Raw. Sample IDs are taken from the subcolumn prefixes. The data transformations in prepdata are an integral part of the SNPMClust methodology.

Value

A list with the following components:

SNP

Character vector of SNP IDs ("rs numbers").

SampleID

Character vector of sample ID numbers, taken from subcolumn prefixes.

P

Length of SNP.

N

Length of SampleID.

Theta

Numeric PxN matrix of Theta subcolumns.

R

Numeric PxN matrix of R subcolumns.

GType

CharacterPxN matrix of GType subcolumns.

Score

Numeric PxN matrix of Score subcolumns.

X.Raw

Numeric PxN matrix of X.Raw subcolumns.

Y.Raw

Numeric PxN matrix of Y.Raw subcolumns.

X

Numeric PxN matrix of X subcolumns.

Y

Numeric PxN matrix of Y subcolumns.

logratio

Numeric PxN matrix of normalized signal intensity log-ratios.

R.trans

Numeric PxN matrix of Box-Cox-transformed signal magnitudes.

Author(s)

Stephen W. Erickson serickson@rti.org with Joshua C. Callaway joshcllw@gmail.com

References

Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02

Examples

1
2

superRhero4/SNPMClust documentation built on May 30, 2019, 8:40 p.m.