Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/crlmmillumina.R
Genotyping of Illumina Infinium II arrays. This function provides CRLMM/KRLMM genotypes and confidence scores for the the polymorphic markers and is a required step prior to copy number estimation.
1 2 3 4 
cnSet 
An object of class 
mixtureParams 

probs 
'numeric' vector with priors for AA, AB and BB. 
SNRMin 
'numeric' scalar defining the minimum SNR used to filter out samples. 
recallMin 
Minimum number of samples for recalibration. 
recallRegMin 
Minimum number of SNP's for regression. 
verbose 
'logical.' Whether to print descriptive messages during processing. 
returnParams 
'logical'. Return recalibrated parameters from crlmm. 
badSNP 
'numeric'. Threshold to flag as bad SNP (affects batchQC) 
gender 
integer vector ( male = 1, female =2 ) or missing, with same length as filenames. If missing, the gender is predicted. 
DF 
'integer' with number of degrees of freedom to use with tdistribution. 
cdfName 

nopackage.norm 
character string specifying normalization to be used when 
call.method 
character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm'). 
trueCalls 
matrix specifying known Genotype calls for a subset of samples and features(1  AA, 2  AB, 3  BB). 
The genotype calls and confidence scores are written to
file using ff
protocols for I/O. For the most part,
the calls and confidence scores can be accessed as though the
data is in memory through the methods snpCall
and
snpCallProbability
, respectively.
The genotype calls are stored using an integer representation: 1
 AA, 2  AB, 3  BB. Similarly, the call probabilities are
stored using an integer representation to reduce file size using
the transformation 'round(1000*log2(1p))', where p is the
probability. The function i2P
can be used to convert the
integers back to the scale of probabilities.
An optional trueCalls
argument can be provided to KRLMM method
which contains known genotype calls(can contain some NAs) for some
samples and SNPs. This will used to compute KRLMM parameters by calling
vglm
function from VGAM
package.
The KRLMM method makes use of functions provided in parallel
package to speed up the process. It by default initialises up to
8 clusters. This is configurable by setting up an option named
"krlmm.cores", e.g. options("krlmm.cores" = 16).
Logical. If the genotyping is completed, the value 'TRUE' is
returned. Note that assayData
elements 'call' and
'callProbability' are updated on disk. Therefore, the genotypes and
confidence scores can be retrieved using accessors for the
CNSet
class.
R. Scharpf
crlmm
, snpCall
,
snpCallProbability
, annotationPackages
1 2  ## See the 'illumina_copynumber' vignette in inst/scripts of
## the source package

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