callValleyDistance: Calculate the inter-valley distance of insert size

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Calculate the inter-valley distance of insert size

Description

Calculate the inter-valley distance of insert size

Usage

callValleyDistance(
  path = getwd(),
  groups,
  limit,
  outfmt,
  summary,
  mincount,
  input_type,
  ...
)

Arguments

path	The root folder containing all groups folders, default is the present working folder.
groups	The name of the groups, the input value should be vector, e.g. groups = c('group1','group2'), default is all folders in the folder path.
limit	The insert size range that will be focused on, default value is 'limit = c(35,135)'.
outfmt	The output format, could specify as 'list' or 'dataframe' or 'df', default is dataframe.
summary	If TRUE, summarize the output.
mincount	The minimum count value of inter-valley distance.
input_type	Character. The input file format should be 'picard' or 'bam', or 'cfdnapro'. The bam files has to be marked duplicates.
...	Further arguments passed to or from other methods.

Value

The inter-valley distance in a list or dataframe.

Author(s)

Haichao Wang

Examples

# Get the path to example data.
path <- examplePath("groups_picard")
# Calculate the inter-valley distance.
df <- callValleyDistance(path = path)

hw538/cfDNAPro documentation built on Aug. 13, 2024, 2:58 p.m.