segmentByPSCB: Segmentation data with PSCBS

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

Segmentation data with PSCBS

Description

Segmentation data with PSCBS

Usage

segmentByPSCB(sample_transformed_sl)

Arguments

sample_transformed_sl

dataframe of z-transformed SLRatio

Value

Dataframe of segmentation result

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)

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