callPeakDistance: Calculate the inter-peak distance of insert size

View source: R/callPeakDistance.R

callPeakDistanceR Documentation

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 Aug. 13, 2024, 2:58 p.m.