qualimap: Extract Qualimap summary tables

In openanalytics/ggqualimap: Plots of Statistics Collected by Qualimap from RNASeq Data

Description

qualimap function parses all the summary statistics of reports produced by Qualimap 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

qualimap(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.

• type - one of "summary", "coverage_high", "coverage_low" and "coverage_total" usually. See vignette for an example 'sample_info' file.

  For html files, type is "summary" and "txt" files, one of the coverage types mentioned above should be provided.

  Note that there may be other types of summary statistic file generated by Qualimap. It is possible to provide a custom type for those files, and qualimap() function would generate the data, but plots are only implemented for summary tables in the html file and all coverage files. This means you will have to implement your own functions to plot those summary statistics.

• path - full path to the qualimap summary report, i.e., html and/or coverage_*.txt files, for each sample.

  If just the file name (without path) 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 qualimap which inherits from "data.table", with two columns: param and value, where value is a list of "data.table"s.

See Also

plot_read_alignment plot_bias_profile plot_coverage_profile plot_junction_analysis plot_genomic_origin

Examples

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

openanalytics/ggqualimap documentation built on May 24, 2019, 2:28 p.m.