Calculate log R ratios and B allele frequencies from
calculateRBaf(object, batch.name, chrom)
A character string indicating the batch. If
missing, log R ratios and B allele frequencies are calculated for all
batches in the
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
batch.name must be a value in
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.
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.
Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping (2006), Genome Research
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data(cnSetExample) baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF")) hist(baf.lrr[["baf"]][]/1000, breaks=100) hist(baf.lrr[["lrr"]][]/100, breaks=100) ## Not run: library(ff) baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF")) class(baf.lrr[["baf"]][]) ## ff_matrix class(baf.lrr[["lrr"]][]) ## ff_matrix ## End(Not run)
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