paulklemm / seqc

seqc

seqc provides quality control figures of cuffdiff results using the cummeRbund package. It produces a static HTML report. Optionally you can output the resulting figures separately.

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• Installation
• Example
• Build Package
• Links & Additional Information
  • Make R aware of Bioconductor package dependencies
  • Credits

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Installation

You can install the development version of seqc using:

# install.packages('devtools')
devtools::install_github("paulklemm/seqc")

Example

Create a static HTML report based on a cuffdiff output and save all generated figures separately in the output_path.

library(seqc)
createHTMLReport(
  cuffdiff_path = '/beegfs/scratch/bruening_scratch/pklemm/htseq-tools-test/cuffdiff_output/TuUp',
  output_path = '/beegfs/scratch/bruening_scratch/pklemm/seqcOutput',
  save_plots = TRUE,
  save_width = 10,
  save_height = 10,
  save_format = 'pdf'
)

Build Package

If you want to customize the image, download this repository, adapt the code and run the following code to build and install it.

roxygen2::roxygenise(); devtools::build(); devtools::install()

Links & Additional Information

These information are not required for running the script and comprise lessons learned and hopefully useful information for fellow R users.

Make R aware of Bioconductor package dependencies

This tool relies on Bioconductor packages. To make R aware that some packages are to be downloaded from bioconductor you can use a trick of adding biocViews: in your DESCRIPTION file (see DESCRIPTION). This was described in this issue.

Credits

• This package adapts code provided by the cummeRbund Manual
• It also adapts code of the QC.R script of the mpg-age-bioinformatics htseq-tools

seqc's Issues

Add note on wrong output of sigMatrix

The cummeRbund sigMatrix outputs wrong counts. The issue is unaddressed by the developer (https://support.bioconductor.org/p/78197/).

Therefore, add note that the matrix is only a rough overview or calculate by hand.

Add nicer heat map

Add heat map such as the following:

Source

http://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html

Fix saving for base plots

Not working:

cuff %>% genes() %>% csDendro() %>%
  saveAndPrint('csDendogram', is_ggplot = FALSE)
cuff %>% genes() %>% csDendro(replicates = TRUE) %>%
  saveAndPrint('csDendogramReplicates', is_ggplot = FALSE)

Check saveReturnPlot