plot_distance_matrix: Plot Distance Matrix from CNVCalling

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

Plot Distance Matrix from CNVCalling

Description

Plot Distance Matrix from CNVCalling

Usage

plot_distance_matrix(cnvcall)

Arguments

cnvcall

cnvcalling result from function call_cnv.R

Value

ggplot object ; distance matrix per cnvcalling solution

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)
plot_distance_matrix(sample_cnv)

Pitithat-pu/cfdnakit documentation built on April 5, 2024, 8:50 p.m.