breaks {VanillaICE} | R Documentation |
Identify breakpoints: physical position of breaks, number of SNPs in region, and the called hidden state.
breaks(x, states, position, chromosome, sampleNames, chromosomeAnnotation = NULL, verbose = FALSE)
x |
Locus X sample matrix of hidden states where the hidden states are represented as integers |
states |
Labels for the hidden states |
position |
Physical position of loci |
chromosome |
integer indicating chromosome (23=X) |
sampleNames |
sample labels |
chromosomeAnnotation |
chromosome annotation. see details |
verbose |
verbose output |
One may provide their own chromosome annotation with centromere start and stop sites. The format must be the same as the chromosomeAnnotation dataset in the R package SNPchip.
data.frame
sample |
sample label |
chr |
chromosome (23 = X) |
start |
starting physical position of segment |
end |
last physical position of segment |
nbases |
number of bases in segment |
nprobes |
number of probes in segment |
state |
label for the state of the segment |
R. Scharpf
x <- matrix(rep(c(1, 2, 3, 1, 2), each=50), ncol=1) breaks(x, states=c("0", "1", "2"), position=1:nrow(x), chromosome=1, sampleNames="A")