compareMethods: Compare copy number calling methods

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Compare copy number calling methods

Description

Compare two sets of aneuHMM objects generated by different methods (see option method of findCNVs).

Usage

compareMethods(models1, models2)

Arguments

models1	A list of aneuHMM objects or a character vector with files that contain such objects.
models2	A list of aneuHMM objects or a character vector with files that contain such objects. IDs of the models must match the ones in models1.

Value

A data.frame with one column 'concordance' which gives the fraction of the genome that is called concordantly between both models.

Author(s)

Aaron Taudt

Examples

## Get a list of HMMs
folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
files <- list.files(folder, full.names=TRUE)
## Compare the models with themselves (non-sensical)
df <- compareMethods(files, files)
head(df)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.