Paper: Identification and correction of sample mix-ups in expression genetic data
The full manuscript (with supplementary tables and figures) is here.
I'm still working out how to include the data, or links to the data (because they're about 2 GB compressed). At the moment, this isn't fully reproducible.
The data are available at the Mouse Phenome Database, though not in exactly the form used in this repository.
The primary manuscript files are
The Perl script
adds all of the legends, and then the
.Rnw file is run through
knitr to create a
LaTeX file, and the two LaTeX files are sent through
xelatex, respectively, to create PDFs.
Makefile tells the full story.
Analysis/R subdirectory has an
asciidoc file for the analyses
in the work. That directory has its own
Cached intermediate results are available at figshare:
(This contains a bunch of
.RData files that go in
- Python 2.7
- GNU make
- R packages: knitr, qtl, broman, lineup, ascii, data.table, igraph, beeswarm, RColorBrewer
- Do clean tests, with and without the intermediate files