backtransformAlleleRatiosByCentroids.matrix: Reverse transform of angular signals

In HenrikBengtsson/aroma.illumina: Analysis of Illumina microarray data [A DRAFT - TRUE]

Description

Reverse transform of angular signals.

Usage

## S3 method for class 'matrix'
backtransformAlleleRatiosByCentroids(beta, mu, truncate=FALSE, ...)

Arguments

beta	An JxI numeric matrix consisting of fractional signals for J SNPs across I samples.
mu	An JxC numeric matrix of fractional locations for C=2 or C=3 centroids.
truncate	If TRUE, the fractional signals are truncated to [0,1].
...	Not used.

Value

Returns an JxI numeric matrix of backtransformed fractional signals.

B Allele Fractions by Peiffer et al. (2007)

In [2], the authors describe how to normalize B Allele Fractions (BAFs) based on predefined linear interpolation. This method, which is used in the Illumina's BeadStudio software, is also described in [1]. That method is obtained by passing θ of [1] and [2] as argument beta while using a Jx3 mu centroid matrix and truncate=TRUE.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

References

[1] Illumina, BeadStudio Genotyping Module v3.2 - User Guide, Illumina Inc., Part \#11284301, Rev. A, 2007, pp 114–115.
[2] Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping, Genome Research, 2006, 16.

Examples

## Not run: 
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Example: Illumina HumanHap550 SNP data
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Predefined genotype centroids for 5 SNPs
mu <- matrix(c(
  0.0042, 0.7057, 0.9933,
  0.0001, 0.5039, 0.9929,
  0.0195, 0.7133, 0.9652,
  0.0111, 0.4507, 0.9850,
  0.0036, 0.5049, 0.9817
), nrow=5, ncol=3, byrow=TRUE);
colnames(mu) <- c("AA", "AB", "BB");
rownames(mu) <- c("rs10013734", "rs10013737", "rs10013782", "rs10013797", "rs10013819");


# Some data
theta <- matrix(c(
  -0.0042,
  0.7057,
  0.9933,
  0.5039,
  0.0111
), nrow=5, ncol=1, byrow=TRUE);

# B Allele Fractions (BAFs) according to Peiffer et al. (2007)
thetaN <- backtransformAlleleRatiosByCentroids(theta, mu=mu, truncate=TRUE)


 
## End(Not run)

HenrikBengtsson/aroma.illumina documentation built on May 7, 2019, 1:55 a.m.