callMode: Calculate the mode fragment size of each sample

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

Calculate the mode fragment size of each sample

Description

Calculate the mode fragment size of each sample

Usage

callMode(
  path,
  groups,
  outfmt = "df",
  order = groups,
  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.
outfmt	The output format, 'list' or 'dataframe' or 'df', default is dataframe.
order	The order in the sorted output, default value equals to 'groups' parameter.
summary	Summarize the dataframe result by calculating each mode size and its count number. Default value is False.
mincount	Minimum count number of each mode size in the summarized output. Only significant when 'summary = TRUE'.
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 valley distance in list or dataframe format.

Author(s)

Haichao Wang

Examples

# Get the path to example data.
path <- examplePath("groups_picard")
# Calculate the mode.
df <- callMode(path = path)

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