calculateRBaf {crlmm} | R Documentation |
Calculate log R ratios and B allele frequencies from
a CNSet
object
calculateRBaf(object, batch.name, chrom)
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
|
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.
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.
Lynn Mireless
Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping (2006), Genome Research
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)