plot_fragment_dist: Plot Fragment-length Distribution

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

Plot Fragment-length Distribution

Description

Plot Fragment-length Distribution

Usage

plot_fragment_dist(readbam_list, maximum_length = 550, minimum_length = 20)

Arguments

readbam_list	List; A list containing SampleBam object/objects from the read_bamfile function
maximum_length	Int; Maximum length of fragment. cfDNA fragment longer than this value will not be considered; Default 550
minimum_length	Int; Minimum length of fragment. cfDNA fragment shorter than this value will not be considered; Default 20

Value

distribution plot

Examples

example_file <-  system.file("extdata","example_patientcfDNA_SampleBam.RDS",package = "cfdnakit")
sample_bambin <- readRDS(example_file)

### adding more samples to the plot
example_file2 <-  system.file("extdata","BH01_CHR15.SampleBam.rds",package = "cfdnakit")
control_bambin <- readRDS(example_file2)
readbam_list <- list(plasma1 = sample_bambin, Healthy.blood.plasma=control_bambin)
plot_fragment_dist(readbam_list)

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