qc_read_collection: Read a collection of FastQC data files

View source: R/qc_read_collection.R

qc_read_collectionR Documentation

Read a collection of FastQC data files


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


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



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


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


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".


logical value. If TRUE, print filename when reading.


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


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


# 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.