Description Usage Arguments Details Value Author(s) References
View source: R/cnrmafunctions.R
Locus and allelespecific estimation of copy number.
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object 
object of class 
MIN.SAMPLES 
'Integer'. The minimum number of samples in a batch. Bathes with fewer than MIN.SAMPLES are skipped. Therefore, samples in batches with fewer than MIN.SAMPLES have NA's for the allelespecific copy number and NA's for the linear model parameters. 
SNRMin 
Samples with low signal to noise ratios are excluded. 
MIN.OBS 
For a SNP with with fewer than 
DF.PRIOR 
The 2 x 2 covariance matrix of the background and signal variances is estimated from the data at each locus. This matrix is then smoothed towards a common matrix estimated from all of the loci. DF.PRIOR controls the amount of smoothing towards the common matrix, with higher values corresponding to greater smoothing. Currently, DF.PRIOR is not estimated from the data. Future versions may estimate DF.PRIOR empirically. 
bias.adj 

prior.prob 
This argument is currently ignored. A numerical vector providing prior probabilities for copy number states corresponding to homozygous deletion, hemizygous deletion, normal copy number, and amplification, respectively. 
seed 
Seed for random number generation. 
verbose 
Logical. 
GT.CONF.THR 
Confidence threshold for genotype calls (0, 1). Calls with confidence scores below this theshold are not used to estimate the withingenotype medians. See Carvalho et al., 2007 for information regarding confidence scores of biallelic genotypes. 
MIN.NU 
numeric. Minimum value for background
intensity. Ignored if 
MIN.PHI 
numeric. Minimum value for slope. Ignored if

THR.NU.PHI 
If 
type 
Character string vector that must be one or more of "SNP", "NP", "X.SNP", or "X.NP". Type refers to a set of markers. See details below 
fit.linearModel 
Logical. If TRUE, a linear model is fit to estimate the parameters for computing the absolute copy number. If FALSE, we compute the batchspecific, withingenotype median and MAD at polymorphic loci and the median and MAD at nonpolymorphic loci. 
We suggest a minimum of 10 samples per batch for using
crlmmCopynumber
. 50 or more samples per batch is preferred
and will improve the estimates.
The functions crlmmCopynumberLD
and
crlmmCopynumber2
have been deprecated.
The argument type
can be used to specify a subset of
markers for which the copy number estimation algorithm is run.
One or more of the following possible entries are valid: 'SNP',
'NP', 'X.SNP', and 'X.NP'.
'SNP' referers to autosomal SNPs.
'NP' refers to autosomal nonpolymorphic markers.
'X.SNP' refers to SNPs on chromosome X.
'X.NP' refers to autosomes on chromosome X.
However, users must run 'SNP' prior to running 'NP' and 'X.NP',
or specify type = c('SNP', 'X.NP')
.
The value returned by the crlmmCopynumber
function
depends on whether the data is stored in RAM or whether the data
is stored on disk using the R package ff
for reading /
writing. If uncertain, the first line of the show
method
defined for CNSet
objects prints whether the
assayData
elements are derived from the ff
package
in the first line. Specifically,
 if the elements of the batchStaticts
slot in the
CNSet
object have the class "ff_matrix" or "ffdf", then
the crlmmCopynumber
function updates the data stored on
disk and returns the value TRUE
.
 if the elements of the batchStatistics
slot in the
CNSet
object have the class 'matrix', then the
crlmmCopynumber
function returns an object of class
CNSet
with the elements of batchStatistics
updated.
R. Scharpf
Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of highdensity oligonucleotide SNP array data. Biostatistics. 2007 Apr;8(2):48599. Epub 2006 Dec 22. PMID: 17189563.
Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15;26(2):2429.
Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, and Irizarry RA, Biostatistics. Biostatistics, Epub July 2010.
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