summary.CNVresults: Explore CNV calling results prior filtering

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

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)

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.