callPeakDistance: Calculate the inter-peak 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-peak distance of insert size

Description

Calculate the inter-peak distance of insert size

Usage

callPeakDistance(
  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, a 'list' or 'dataframe'. Default is dataframe.
summary	If TRUE, summarize the output.
mincount	The minimum count value of inter-peak distance in the summary.
input_type	Character. The input file format, should be one of these: 'picard', 'bam', 'cfdnapro'. The bam files has to be marked duplicates.
...	Further arguments passed to or from other methods.

Value

The function returns the inter peak distance in list or dataframe format.

Author(s)

Haichao Wang

Examples

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

hw538/cfDNAPro documentation built on Nov. 28, 2024, 12:13 p.m.