get_solution_table: Get summarised table of cnv solutions

In Pitithat-pu/cfDNAkit: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Get summarised table of cnv solutions

Description

Get summarised table of cnv solutions

Usage

get_solution_table(cnv_solutions)

Arguments

cnv_solutions

cnvcalling result from function call_cnv.R

Value

Dataframe of solution table

Examples

#'
### Loading example SampleBam file
example_file <-  system.file("extdata","example_patientcfDNA_SampleBam.RDS",package = "cfdnakit")
sample_bambin <- readRDS(example_file)
### Example PoN
PoN_rdsfile <- system.file("extdata","ex.PoN.rds",package = "cfdnakit")
pon_profiles <- readRDS(PoN_rdsfile)
sample_profile <- get_fragment_profile(sample_bambin,sample_id = "Patient1")

sample_zscore <- get_zscore_profile(sample_profile,pon_profiles)

sample_zscore_segment <- segmentByPSCB(sample_zscore)

sample_cnv <- call_cnv(sample_zscore_segment,sample_zscore, tfs=c(0.1,0.3),ploidies=c(1.5,2), MaxCN=3)
get_solution_table(sample_cnv)

Pitithat-pu/cfDNAkit documentation built on Oct. 2, 2024, 7:31 a.m.