SnpArrayExperiment-class {VanillaICE} | R Documentation |
A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference
Constructor for SnpArrayExperiment
SnpArrayExperiment(cn, baf, rowRanges = GRanges(), colData = DataFrame(), isSnp = logical(), ...) ## S4 method for signature 'missing' SnpArrayExperiment(cn, baf, rowRanges = GRanges(), colData = DataFrame(), isSnp = logical(), ...) ## S4 method for signature 'matrix' SnpArrayExperiment(cn, baf, rowRanges = GRanges(), colData = DataFrame(row.names = colnames(cn)), isSnp = logical(), ...)
cn |
matrix of copy number estimates (e.g., log R ratios) |
baf |
matrix of B allele frequencies |
rowRanges |
GRanges object for SNPs/nonpolymorphic markers |
colData |
DataFrame containing sample-level covariates |
isSnp |
logical vector indicating whether marker is a SNP |
... |
additional arguments passed to |
## empty container SnpArrayExperiment() data(snp_exp) # example SnpArrayExperiment(cn=lrr(snp_exp), baf=baf(snp_exp), rowRanges=rowRanges(snp_exp))