callValleyDistance: Calculate the inter-valley distance of insert size

View source: R/callValleyDistance.R

callValleyDistanceR Documentation

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.