fastqc: Extract FastQC summary tables

In openanalytics/ggfastqc: Generate Summary Plots of FastQC Reports

Description

fastqc function parses all the summary statistics of reports produced by FastQC tool and returns a data.table with two columns: param and value.

Each row of the value column contains the data corresponding to that param, and is itself a data.table.

Usage

fastqc(sample_info)

Arguments

sample_info

Full path to file containing details about samples and their paths.

Details

The file provided to sample_info argument should contain at least these three columns:

• sample - contains the sample name.

• pair - in case of paired end reads, 1 or 2 corresponding to first and second pair, and in case of single end reads, NA.

• path - full path to the fastqc summary report (.txt file) for each sample.

  If just the file name (.txt) is provided, it is assumed that the file is in the same folder as the input file provided to sample_info argument.

It can also optionally contain a group column. If present, the plots generated will take it into account and color / facet accordingly.

Value

An object of class fastqc which inherits from "data.table", with two columns: param and value, where value is a list of "data.table"s.

See Also

plot_dup_stats plot_gc_stats plot_sequence_quality plot_total_sequence_stats

Examples

path = system.file("tests/fastqc-sample", package="ggfastqc")
obj = fastqc(sample_info = file.path(path, "annotation.txt"))

openanalytics/ggfastqc documentation built on May 24, 2019, 2:27 p.m.