qc_aggregate {fastqcr}

Aggregate FastQC Reports for Multiple Samples

Description

Aggregate multiple FastQC reports into a data frame.

Usage

qc_aggregate(qc.dir = ".", progressbar = TRUE)

## S3 method for class 'qc_aggregate'
summary(object, ...)

qc_stats(object)

Arguments

qc.dir

path to the FastQC result directory to scan.

progressbar

logical value. If TRUE, shows a progress bar.

object

an object of class qc_aggregate.

...

other arguments.

Value

• qc_aggregate() returns an object of class qc_aggregate which is a (tibble) data frame with the following column names:

  • sample: sample names

  • module: fastqc modules

  • status: fastqc module status for each sample

  • tot.seq: total sequences (i.e.: the number of reads)

  • seq.length: sequence length

  • pct.gc: % of GC content

  • pct.dup: % of duplicate reads

• summary: Generates a summary of qc_aggregate. Returns a data frame with the following columns:

  • module: fastqc modules

  • nb_samples: the number of samples tested

  • nb_pass, nb_fail, nb_warn: the number of samples that passed, failed and warned, respectively.

  • failed, warned: the name of samples that failed and warned, respectively.

• qc_stats: returns a data frame containing general statistics of fastqc reports. columns are: sample, pct.dup, pct.gc, tot.seq and seq.length.

Functions

• qc_aggregate(): Aggregate FastQC Reports for Multiple Samples

• qc_stats(): Creates general statistics of fastqc reports.

Examples

# Demo QC dir
qc.dir <- system.file("fastqc_results", package = "fastqcr")
qc.dir

# List of files in the directory
list.files(qc.dir)

# Aggregate the report
qc <- qc_aggregate(qc.dir, progressbar = FALSE)
qc

# Generates a summary of qc_aggregate
summary(qc)

# General statistics of fastqc reports.
qc_stats(qc)