snp.cor: Correlations with columns of a SnpMatrix

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/structure.R

Description

This function calculates Pearson correlation coefficients between columns of a SnpMatrix and columns of an ordinary matrix. The two matrices must have the same number of rows. All valid pairs are used in the computation of each correlation coefficient.

Usage

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snp.cor(x, y, uncertain = FALSE)

Arguments

x

An N by M SnpMatrix

y

An N by P general matrix

uncertain

If TRUE, uncertain genotypes are replaced by posterior expectations. Otherwise these are treated as missing values

Details

This can be used together with xxt and eigen to calculate standardized loadings in the principal components

Value

An M by P matrix of correlation coefficients

Note

This version cannot handle X chromosomes

Author(s)

David Clayton [email protected]

See Also

xxt

Examples

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# make a SnpMatrix with a small number of rows
data(testdata)
small <- Autosomes[1:100,]
# Calculate the X.X-transpose matrix
xx <- xxt(small, correct.for.missing=TRUE)
# Calculate the principal components
pc <- eigen(xx, symmetric=TRUE)$vectors
# Calculate the loadings in first 10 components */
loadings <- snp.cor(small, pc[,1:10])

NikNakk/snpStats documentation built on May 9, 2017, 2:15 p.m.