qc_read_collection: Read a collection of FastQC data files

Description Usage Arguments Value Author(s) Examples

View source: R/qc_read_collection.R

Description

A wrapper function around qc_read to read multiple FastQC data files at once.

Usage

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qc_read_collection(files, sample_names, modules = "all", verbose = TRUE)

Arguments

files

A character vector of paths to the files to be imported.

sample_names

A character vector of length equals that of the first argument files

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

A list of tibbles containing the data of specified modules form each file.

Author(s)

Mahmoud Ahmed, mahmoud.s.fahmy@students.kasralainy.edu.eg

Examples

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# extract paths to the demo files
qc.dir <- system.file("fastqc_results", package = "fastqcr")
qc.files <- list.files(qc.dir, full.names = TRUE)

# read all modules in all files
qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:5, sep = ''))


# read a specified module in all files
qc <- qc_read_collection(qc.files, 
    sample_names = paste('S', 1:5, sep = ''),
    modules = "Per base sequence quality")

fastqcr documentation built on May 2, 2019, 2:13 a.m.