qc_read: Read FastQC Data

Description Usage Arguments Value Examples

View source: R/qc_read.R

Description

Read FastQC data into R.

Usage

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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

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# 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 May 2, 2019, 2:13 a.m.