Description Usage Arguments Details Value Author(s) See Also
View source: R/SnpSetIlluminaGenotypes.R
Using pairings of normal and tumor samples the LOH pattern is determined
1 2 3 | calculateLOH(object, grouping, NorTum = "NorTum", ...)
calculateLair(object, grouping = NULL, NorTum = "NorTum", min.intensity = NULL,
use.homozygous.avg = FALSE)
|
object |
SnpSetIllumina object |
grouping |
Factor to show which samples belong together (are of the same individual) |
NorTum |
character vector or factor. Elements containing "N" are considered to be the normal sample |
min.intensity |
numeric |
use.homozygous.avg |
logical |
... |
extra arguments for |
The heterozygous SNPs of the normal sample are inspected for changes. SNPs where the genotype of the test sample are homozygous are set to TRUE
For calculateLOH a SnpSetIllumina object with loh
and nor.gt
matrices in assayData.
loh
is a logical matrix, and nor.gt
is a character matrix containing
the genotypes of the corresponding normal sample
For calculateLair a SnpSetIllumina object with lair
matrix in assayData. lair is the lesser
allele intensity ratio. If a corresponding normal sample is found, it is taken as reference. Else the
genotypes of normal samples are taken as a reference
Jan Oosting
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