Description Usage Arguments Details Value Author(s) References Examples
Converts and transforms data from GenomeStudio output into form that can be handled by the function snpmclust
.
1 | prepdata(rawdata)
|
rawdata |
Data frame taken from an import of GenomeStudio full data table. |
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.
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. |
Stephen W. Erickson serickson@rti.org with Joshua C. Callaway joshcllw@gmail.com
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
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