callSize {cfDNAPro} | R Documentation

## Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or each group

### Description

Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or each group

### Usage

    callSize(path, groups, outfmt, 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, could specify as '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 function returns the insert size metrics of each group in list or dataframe format.

### Author(s)

Haichao Wang

### Examples

    # Get the path to example data.
    path <- examplePath("groups_picard")
    # Calculate the size.
    df <- callSize(path = path)

[Package cfDNAPro version 1.0.0 Index]