Description Usage Arguments Value Author(s) Examples
View source: R/qc_plot_collection.R
Plot FastQC data of multiple samples
1 | qc_plot_collection(qc, modules = "all")
|
qc |
An object of class qc_read_collection or a path to the sample zipped fastqc result files. |
modules |
Character vector containing the names of fastqc modules for which you want to import the data. Default is all. Allowed values include one or the combination of:
Partial match of module names allowed. For example, you can use modules = "GC content", instead of the full names modules = "Per sequence GC content". |
Returns a list of ggplots containing the plot for specified modules..
Mahmoud Ahmed, mahmoud.s.fahmy@students.kasralainy.edu.eg
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | 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 = ''))
# Plot per sequence GC content
qc_plot_collection(qc, "Per sequence GC content")
# Per base sequence quality
qc_plot_collection(qc, "Per base sequence quality")
# Per sequence quality scores
qc_plot_collection(qc, "Per sequence quality scores")
# Per base sequence content
qc_plot_collection(qc, "Per base sequence content")
# Sequence duplication levels
qc_plot_collection(qc, "Sequence duplication levels")
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