computeCopynumber {crlmm}R Documentation

Computes copy number

Description

A function that transforms the quantile-normalized fluorescence intensities of the polymorphic and nonpolymorphic probes to a copy number scale.

Usage

computeCopynumber(chrom, A, B, calls, conf, NP, plate, MIN.OBS=1, 
envir, P, DF.PRIOR = 50, CONF.THR = 0.99, bias.adj=FALSE,
priorProb, gender=NULL, SNR, SNRmin, seed=123, cdfName="genomewidesnp6",
verbose=TRUE, ...)

Arguments

chrom Chromosome (an integer). Use 23 for X and 24 for Y.
A The A allele intensities from snprma
B The B allele intensities from snprma
calls The genotype calls from crlmm
conf The genotype confidence scores from crlmm
NP The quantile normalized intensities of the nonpolymorphic probes
plate The bach variable. Should be the same length as the number of columns in A
MIN.OBS Integer: The minimum number of observations in a genotype cluster for which a SNP is deemed complete.
envir An environment to save intermediate objects
P Mainly for debugging a particular plate/batch.
DF.PRIOR The degrees of freedom for the prior. Higher numbers will shrink the variance and correlation more.
CONF.THR A threshold for the genotype confidence scores. Genotypes with scores below the threshold are ignored when computing SNP-specific within-genotype estimates of location and scale.
bias.adj Logical: whether to adjust the location and scale parameters to account for biases due to common copy number variants. This is a SNP-specific adjustment. Parameters for background and slope must have already been estimated and available from the environment variable.
priorProb Numerical vector of length 4. The prior probability of each copy number state (0, 1, 2, 3, and 4). The default is a uniform prior. Ignored if bias.adj=FALSE
gender Gender of subjects. If not specified, we predict the gender from the X chromosome.
SNR Signal to noise ratio from crlmm.
SNRmin The minimum value for the SNR – we suggest 5. Samples with SNR below SNRmin are excluded.
seed Seed used for random samples
cdfName Annotation package
verbose Logical: verbose output
... Currently ignored

Details

Parameters for copy number are estimated using a linear model based on the diallelic genotype calls. No training data is used to estimate model parameters. Therefore, this function requires at least 10 samples to estimate copy number. For small sample sizes (e.g., 10 - 30 samples), this function will impute model parameters for a large number of loci and the precision of the estimates will be reduced.

Key assumption:

- we assume that the median copy number at any given locus is two for each batch. This assumption may not be appropriate for many datasets (e.g., a cancer dataset without normals processed in the same batch).

The developmental version of this package available from Bioconductor has many improvements to this function.

Value

All objects created by this function are stored in the environment passed to this function. In addition, each of the elements are specific to the chromosome(s) specified by the argument chrom. For instance the element A is the matrix of quantile-normalized intensities for the A-allele on chromosome(s) chrom. The element of this environment are as follows

A Matrix of quantile-normalized intensities for the A-allele
B Matrix of quantile-normalized intensities for the A-allele
CA Copy number estimate for the A-allele (x 100)
CB Copy number estimate for the B-allele (x 100)
calls CRLMM genotype calls (AA=1, AB=2, BB=3)
chrom Integer(s) indicating the chromosome(s)
cnvs Names of the nonpolymorphic probes. These are the rownames of NP and CT.
conf CRLMM confidence scores for the genotypes: 'round(-1000*log2(1-p))'
corr Correlation of the A and B alleles for genotypes AB
corrA.BB Correlation of A and B alleles for genotypes BB
corrB.AA Correlation of A and B alleles for genotypes AA
CT Copy number estimates for nonpolymorphic probe. See cnvs for the rownames.
CT.sds Standard deviation estimates for CT
npflags Flags for the nonpolymorphic probes.
Ns The number of observations for each genotype/plate
nuA Background/cross-hyb for the A allele (plate- and locus-specific)
nuB Background/cross-hyb for the B allele (plate- and locus-specific)
nuT Background for the nonpolymorphic probes (plate- and locus-specific)
phiA Slope for the A allele (plate- and locus-specific)
phiB Slope for the B allele (plate- and locus-specific)
phiT Slope for the nonpolymorphic probes (plate- and locus-specific)
plate Factor indicating batch (same length as number of cel files)
sig2A Variance estimate for the A-allele signal (plate- and locus-specific)
sig2B Variance estimate for the B-allele signal (plate- and locus-specific)
sig2T Variance estimate for the nonpolymorphic signal (plate- and locus-specific)
snpflags Flags for polymorphic probes
snps Rownames for A, B, CA, CB, ...
sns Sample names – the column names for A, B, ...
steps Steps completed. For internal use.
tau2A Variance estimate for the B-allele background/cross-hyb (plate- and locus-specific)
tau2B Variance estimate for the B-allele background/cross-hyb (plate- and locus-specific)

Author(s)

Rob Scharpf

References

Nothing yet.


[Package crlmm version 1.2.4 Index]