qc_read: Read FastQC Data

In fastqcr: Quality Control of Sequencing Data

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")

fastqcr documentation built on March 7, 2023, 8:16 p.m.