callMode: Calculate the mode fragment size of each sample

View source: R/callMode.R

callModeR Documentation

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.