Get quality control metrics from YAML

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

Michael Steinbaugh

Examples

file <- file.path(bcbioBaseTestsUrl, "summary.yaml")
yaml <- import(file)
#> → Downloading <https://r.acidgenomics.com/testdata/bcbiobase/summary.yaml> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmprBcLWH/MjgbCVQHOG-169651164429374/pipette-10f0e5368f0ab.yaml.
#> → Importing <https://r.acidgenomics.com/testdata/bcbiobase/summary.yaml> using yaml::`yaml.load_file()`.
x <- getMetricsFromYaml(yaml)
#> → Getting sample quality control metrics from YAML.
summary(x)
#> [1] "DataFrame object of length 16 with 0 metadata columns"
colnames(x)
#>  [1] "averageInsertSize"             "duplicates"                   
#>  [3] "duplicationRateOfMapped"       "exonicRate"                   
#>  [5] "intergenicRate"                "intronicRate"                 
#>  [7] "mappedPairedReads"             "mappedReads"                  
#>  [9] "percentGc"                     "qualityFormat"                
#> [11] "rrna"                          "rrnaRate"                     
#> [13] "sequenceLength"                "sequencesFlaggedAsPoorQuality"
#> [15] "totalReads"                    "x5x3Bias"