plot_cnv_solution: Plot Fragment-length profile with CNV calling result

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

Plot Fragment-length profile with CNV calling result

Description

Plot Fragment-length profile with CNV calling result

Usage

plot_cnv_solution(
  cnvcall,
  selected_solution = 1,
  genome = "hg19",
  ylim = c(-30, 30)
)

Arguments

cnvcall	solution results from call_cnv function
selected_solution	solution rank to plot
genome	Character; version of reference genome (default hg19)
ylim	Vector of 2 Int; ylim of plot (default c(-20,20))

Value

ggplot object plot Genomics CNV profile of selected 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_cnv_solution(sample_cnv,selected_solution = 1)

Pitithat-pu/cfdnakit documentation built on Oct. 2, 2024, 8:03 p.m.