Paper: Identification and correction of sample mix-ups in expression genetic data
The full manuscript (with supplementary tables and figures) is here.
Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2015) Identification and correction of sample mix-ups in expression genetic data: A case study. G3 5:2177-2186
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.
Things are a bit tricky. In principle, the
Makefile tells the full
story, but the
Analysis/R subdirectory has an
asciidoc file for the analyses
in the work. That directory has its own
intermediate results are available at figshare:
(This contains a bunch of
.RData files that go in
To compile everything, you can:
Download the cached intermediate results,
samplemixups_rcache.zipand unzip them. This will populate
R CMD BATCH grab_data.R
This will download the primary data files. It's quite slow, as it's 2 GB of data to download.
In the primary directory, run
- 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
The content in this repository is licensed under CC BY.