subsetByCNVprofile: Get IDs of a subset of models

In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description

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.

Usage

subsetByCNVprofile(hmms, profile)

Arguments

hmms	A list of aneuHMM objects or a character vector with files that contain such objects.
profile	A GRanges-class object with metadata column 'expected.state' and optionally columns 'expected.mstate' and 'expected.pstate'.

Value

A named logical vector with TRUE for all models that are concordant with the given profile.

Examples

## 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))

AneuFinder documentation built on Nov. 8, 2020, 7:44 p.m.