Calculate log R ratios and B allele frequencies.
Description
Calculate log R ratios and B allele frequencies from
a CNSet
object
Usage
1  calculateRBaf(object, batch.name, chrom)

Arguments
object 
A 
batch.name 
A character string indicating the batch. If
missing, log R ratios and B allele frequencies are calculated for all
batches in the 
chrom 
Integer indicating which chromosome to process. If
missing, B allele frequencies and log R ratios are calculated for all
autosomal chromosomes and chromosome X that are included in

Details
batch.name
must be a value in batch(object)
. Currently,
one must specify a single batch.name
. If a character vector for
batch.name
is supplied, only the first is evaluated.
TODO: A description of how these values are calculated.
Value
A named list.
baf
: Each element in the baf list is a matrix of B allele
frequencies (one matrix for each chromosome).
lrr
: Each element in the lrr list is a matrix of log R ratios
(one matrix for each chromosome).
The log R ratios were scaled by a factor of 100 and stored as an integer. B allele frequencies were scaled by a factor of 1000 and stored as an integer.
Author(s)
Lynn Mireless
References
Peiffer et al., Highresolution genomic profiling of chromosomal aberrations using Infinium wholegenome genotyping (2006), Genome Research
Examples
1 2 3 4 5 6 7 8 9 10 11  data(cnSetExample)
baf.lrr < suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
hist(baf.lrr[["baf"]][[1]]/1000, breaks=100)
hist(baf.lrr[["lrr"]][[1]]/100, breaks=100)
## Not run:
library(ff)
baf.lrr < suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
class(baf.lrr[["baf"]][[1]]) ## ff_matrix
class(baf.lrr[["lrr"]][[1]]) ## ff_matrix
## End(Not run)
