extract_metrics: Extract tables from a happy_compare object

In Illumina/happyCompare: Reporting toolbox for hap.py output

Description

Extract tables from a happy_compare object and combine into a single data.frame. Appends samplesheet metadata to the original happy results.

Usage

extract_metrics(happy_compare, table = c("summary", "extended", "pr.all",
  "pr.snp.all", "pr.snp.pass", "pr.snp.sel", "pr.indel.all", "pr.indel.pass",
  "pr.indel.sel", "build.metrics"))

Arguments

happy_compare	A happy_compare object.
table	Table of data to extract from each happy_result object. Must be one of: summary, extended, pr.all, pr.snp.all, pr.snp.pass, pr.snp.sel, pr.indel.all, pr.indel.pass, pr.indel.sel, build_metrics.

Value

A data.frame with combined information from the selected happy_result and its samplesheet.

Examples

## Not run: 
summary <- extract_metrics(happy_compare, table = 'summary')
roc <- extract_metrics(happy_compare, table = 'pr.snp.pass')
build_metrics <- extract_metrics(happy_compare, table = 'build.metrics')

## End(Not run)

Illumina/happyCompare documentation built on July 12, 2019, 7:57 p.m.