qc_read {fastqcr}

Read FastQC Data

Description

Read FastQC data into R.

Usage

qc_read(file, modules = "all", verbose = TRUE)

Arguments

file

Path to the file to be imported. Can be the path to either :

• the fastqc zipped file (e.g.: 'path/to/samplename_fastqc.zip'). No need to unzip,

• or the unzipped folder name (e.g.: 'path/to/samplename_fastqc'),

• or the sample name (e.g.: 'path/to/samplename' )

• or the fastqc_data.txt file,

modules

Character vector containing the names of FastQC modules for which you want to import/inspect the data. Default is all. Allowed values include one or the combination of:

• "Summary",

• "Basic Statistics",

• "Per base sequence quality",

• "Per tile sequence quality",

• "Per sequence quality scores",

• "Per base sequence content",

• "Per sequence GC content",

• "Per base N content",

• "Sequence Length Distribution",

• "Sequence Duplication Levels",

• "Overrepresented sequences",

• "Adapter Content",

• "Kmer Content"

Partial match of module names allowed. For example, you can use modules = "GC content", instead of the full names modules = "Per sequence GC content".

verbose

logical value. If TRUE, print filename when reading.

Value

Returns a list of tibbles containing the data for specified modules.

Examples

# Demo file
qc.file <- system.file("fastqc_results", "S1_fastqc.zip",  package = "fastqcr")
qc.file
# Read all modules
qc_read(qc.file)

# Read a specified module
qc_read(qc.file,"Per base sequence quality")