A wrapper function around qc_read to read multiple FastQC data files at once.
qc_read_collection(files, sample_names, modules = "all", verbose = TRUE)
character vector of paths to the files to be imported.
character vector of length equals that of the first argument
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:
"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",
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.
tibbles containing the data of specified modules form each file.
# 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") #> Reading: /private/var/folders/xm/8p6yj4bj6s57n4v_51714lwm0000gp/T/RtmpT6jSz8/temp_libpatha9b37e9f6eab/fastqcr/fastqc_results/S1_fastqc.zip #> Reading: /private/var/folders/xm/8p6yj4bj6s57n4v_51714lwm0000gp/T/RtmpT6jSz8/temp_libpatha9b37e9f6eab/fastqcr/fastqc_results/S2_fastqc.zip