assignBgPriors: Assign the Background Signal Priors for each PM probe

In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description

The function assigns a log-normal prior distribution for background signal to each PM probe on the specified cdf. The prior is estimated based on sequence composition using either MAT or the GC count

Usage

assignBgPriors(celSet, seqFile, bgBins = NULL, bgParam = NULL,
  method = "MAT", path, batchSize = NULL, overWrite = FALSE)

Arguments

celSet	the set of CEL files to be analysed
seqFile	the file with the sequence data for all PM probes. Must contain the xy co-ordinates of each probe & sequence data for each probe.
bgBins	the output of either defineMatBins or defineGcBins.
bgParam	the model parameters as returned by the function fitBackgroundParameters. Not required if using method="GC".
method	only "MAT" & "GC" can be supplied. Defaults to "MAT".
path	the root directory where files should be written. Defaults to the working directory
batchSize	the number of probes to be written to file in batches. Calculated as a function of memory size.
overWrite	logical. Determines whether to over-write any existing .CEL files with new information. If overWrite = FALSE, checks for pre-existing celFiles will be performed & if a complete set matching the supplied celSet is found, this will be used.

Details

This process will create two sets of .CEL files containing the mean (lambda) & standard deviation (delta) for the background priors under the BMEA model for each PM probe contained on the supplied cdf. The priors are based on the assumption that log(B) ~ N(lambda, delta).

The .CEL files will be written to the subdirectories of the path or working directory backgroundPriors/parentName,method,lambda/chipType & backgroundPriors/parentName,method,delta/chipType.

Value

Returns a list with components $lambda & $delta. Each component is an AffymetrixCelSet containing the respective means & sds.

References

H. Bengtsson, K. Simpson, J. Bullard, and K. Hansen, (2008) aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley.

Kapur, K., Xing, Y., Ouyang, Z., Wong, WH. (2007) Exon arrays provide accurate assessments of gene expression Genome Biol. 8(5):R82

Johnson, W.E., Li, W., Meyer, C.A., Gottardo, R., Carroll, J.S., Brown, M., Liu, X.S. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 103:12457-12462

steveped/BMEA documentation built on May 30, 2019, 5:38 p.m.