Get the summary information from Fastqc Files

Read the information from the summary.txt files in each .FastqcFile

# S4 method for class '.FastqcFile'
getSummary(object)

# S4 method for class 'ANY'
getSummary(object)

# S4 method for class 'FastqcData'
getSummary(object)

# S4 method for class 'FastqcDataList'
getSummary(object)

Arguments

object

Can be a FastqcData, FastqcDataList object or a vector of paths to unparsed FastQC reports.

Value

A tibble containing the PASS/WARN/FAIL status for each module, as defined in a FastQC report.

Details

This simply extracts the summary of PASS/WARN/FAIL status for every module as defined by the tool FastQC for each supplied file.

Examples

# Get the files included with the package
packageDir <- system.file("extdata", package = "ngsReports")
fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)

# Load the FASTQC data as a FastqcDataList object
fdl <- FastqcDataList(fl)

# Return a tibble/tibble with the raw information
getSummary(fdl)
#> # A tibble: 72 × 3
#>    Status Category                     Filename     
#>    <chr>  <chr>                        <chr>        
#>  1 PASS   Basic Statistics             ATTG_R1.fastq
#>  2 FAIL   Per base sequence quality    ATTG_R1.fastq
#>  3 WARN   Per tile sequence quality    ATTG_R1.fastq
#>  4 PASS   Per sequence quality scores  ATTG_R1.fastq
#>  5 FAIL   Per base sequence content    ATTG_R1.fastq
#>  6 FAIL   Per sequence GC content      ATTG_R1.fastq
#>  7 PASS   Per base N content           ATTG_R1.fastq
#>  8 PASS   Sequence Length Distribution ATTG_R1.fastq
#>  9 FAIL   Sequence Duplication Levels  ATTG_R1.fastq
#> 10 FAIL   Overrepresented sequences    ATTG_R1.fastq
#> # ℹ 62 more rows