qc_read_collection: Read a collection of FastQC data files

In fastqcr: Quality Control of Sequencing Data

Read a collection of FastQC data files

Description

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

Usage

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, [e-mail]

Examples

# extract paths to the demo files
qc.dir <- system.file("fastqc_results", package = "fastqcr")
qc.files <- list.files(qc.dir, full.names = TRUE)[1:2]
nb_samples <- length(qc.files)


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

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