subsetByCNVprofile {AneuFinder} | R Documentation |
Get the IDs of models that have a certain CNV profile. The result will be TRUE
for models that overlap all specified ranges in profile
by at least one base pair with the correct state.
subsetByCNVprofile(hmms, profile)
hmms |
A list of |
profile |
A |
A named logical vector with TRUE
for all models that are concordant with the given profile
.
## Get results from a small-cell-lung-cancer lung.folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData") lung.files <- list.files(lung.folder, full.names=TRUE) ## Get all files that have a 3-somy on chromosome 1 and 4-somy on chromosome 2 profile <- GRanges(seqnames=c('1','2'), ranges=IRanges(start=c(1,1), end=c(195471971,182113224)), expected.state=c('3-somy','4-somy')) ids <- subsetByCNVprofile(lung.files, profile) print(which(ids))