callMode {cfDNAPro} | R 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'. 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)

[Package cfDNAPro version 1.0.0 Index]