getMetricsFromYaml: Get quality control metrics from YAML

In hbc/bcbioBase: Bcbio Base Functions

Get quality control metrics from YAML

Description

Parse the summary YAML and return quality control metrics.

Usage

getMetricsFromYaml(yaml)

Arguments

yaml	list. YAML metadata.

Value

DataFrame.

Note

Metrics are only generated for a standard RNA-seq run with aligned counts. Fast RNA-seq mode with lightweight counts (pseudocounts) doesn't output the same metrics into the YAML.

Updated 2022-03-07.

Author(s)

Michael Steinbaugh

Examples

file <- file.path(bcbioBaseTestsUrl, "summary.yaml")
yaml <- import(file)
x <- getMetricsFromYaml(yaml)
summary(x)
colnames(x)

hbc/bcbioBase documentation built on Oct. 18, 2023, 1:02 p.m.