callMetrics {cfDNAPro} | R Documentation

## Calculate the metrics of insert size

### Description

Calculate the metrics of insert size

### Usage

    callMetrics(
      path = getwd(),
      groups,
      fun = "all",
      outfmt = "df",
      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 sub-folders in the 'path'.
`fun` | String value, the types of metrics to be calculated. Default is 'all', which means both median and mean values will be returned.
`outfmt` | The output format, a 'list' or 'dataframe' or 'df', default is dataframe.
`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 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 metrics.
    df <- callMetrics(path = path)

[Package cfDNAPro version 1.0.0 Index]