subsetByCNVprofile: Get IDs of a subset of models

Description Usage Arguments Value Examples

View source: R/subsetByCNVprofile.R

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

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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

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## 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))

ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.