plot_transformed_sl: Plot z-tranformed Short/Long-fragment Ratio

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

Plot z-tranformed Short/Long-fragment Ratio

Description

Plot z-tranformed Short/Long-fragment Ratio

Usage

plot_transformed_sl(
  sample_transformed_sl,
  sample_segment_df = NULL,
  ylim = c(-30, 30),
  genome = "hg19"
)

Arguments

sample_transformed_sl	Dataframe z-transformed SLRatio from get_zscore_profile
sample_segment_df	Dataframe segmenation from segmentByPSCB
ylim	plot y-axis limit
genome	Character; version of reference genome (default hg19)

Value

Genome-wide plot of z-transformed SLRatio

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)
plot_transformed_sl(sample_zscore, sample_zscore_segment)
## Change reference genome
plot_transformed_sl(sample_zscore, sample_zscore_segment,genome="hg38")

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