get_fragment_profile: Getting fragment-length information

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

Getting fragment-length information

Description

Getting fragment-length information

Usage

get_fragment_profile(
  readbam_bin,
  sample_id,
  genome = "hg19",
  short_range = c(100, 150),
  long_range = c(151, 250),
  maximum_length = 600,
  minimum_length = 20
)

Arguments

readbam_bin	SampleBam Object
sample_id	Character; Given sample ID
genome	abbreviation of reference genome; namely hg19, mm10. default:hg19
short_range	Vector of 2 Int; Range of fragment length to be defined as short fragment; Default c(100,150)
long_range	Vector of 2 Int; Range of fragment length to be defined as long fragment; Default c(151,250)
maximum_length	Int; Maximum length of fragment. cfDNA fragment longer than this value will not be considered; Default 600
minimum_length	Int; Minimum length of fragment. cfDNA fragment shorter than this value will not be considered; Default 20

Value

SampleFragment Object; Fragment length information for quality check and downstream analysis per bin and summary of sample

Examples

example_file <-  system.file("extdata","example_patientcfDNA_SampleBam.RDS",package = "cfdnakit")
sample_bambin <- readRDS(example_file)
sample_profile <- get_fragment_profile(sample_bambin,sample_id = "Patient1")

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