callValleyDistance {cfDNAPro} | R 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'. 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)

[Package cfDNAPro version 1.0.0 Index]