calculate_CES_score: Calculate CES Score from Segmentation

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

Calculate CES Score from Segmentation

Description

Calculate CES Score from Segmentation

Usage

calculate_CES_score(sample_segmentation)

Arguments

sample_segmentation

Segmentation Dataframe

Value

Numeric; CES score

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)

calculate_CES_score(sample_zscore_segment)

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