summary.CNVresults {CNVgears} | R Documentation

## Explore CNV calling results prior filtering

### Description

Explore CNV calling results prior filtering

### Usage

    ## S3 method for class 'CNVresults'
    summary(object, sample_list, markers, plots_path = NA, ...)

### Arguments

`object,` | a `data.table`, the output of `read_results`.
`sample_list,` | a `data.table`, the output of `read_metadt`.
`markers,` | a `data.table`, the output of `read_NGS_intervals` or `read_finalreport_snps`, depending on the initial data type.
`plots_path,` | path where the plots should be saved, if `NA` no plot is produced.
`...` | compatibility This function produce several summary statistics on the CNVs results in input. Ideally, it should be used interactively, together with `cleaning_filter`. Some information is printed on the console (mostly `summary()` on several characteristics of the results and the cohort), several plots can be produced and saved in the user specified location. Finally the function also return a `data.table` of sample-level summary.

### Value

a `data.table` with summary statistics for the samples in the cohort.

### Examples

    DT <- summary(penn_22, cohort_examples, markers_examples)

[Package CNVgears version 1.0.0 Index]