qc_read_collection {fastqcr}

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")