This is a copy of the programs and scripts (C, perl, R) I developed while working on my dissertation using radiation hybrid data to investigate copy number effects on gene expression using Illumina microarrays.
Code is in drive2, home, home3, media
lib
lib/ - perl modules for manipulating compact binary versions of CGH data
QTL
Mapping of copy number eQTLs. I did this for multiple data sets (human, rat, mouse, dog) and also compared with other data sets such as GNF Novartis (symatlas) and TCGA data.
rhvec
Co-retention of RH markers across different animal panels (human, rat, mouse dog)
useful code
Possibly useful code bits
convert data to binary
Make binary version of CGH data matrix to allow for faster lookup. Perl modules are used to access the data quickly.
linear model
C code for linear regression using GSL and permutation code to derive p value of alpha values.
correlation
I derived how to compute a correlation doing a single pass through the data. Implemented in C.
chi square
C implementation of chi square computation
synteny plot
Create synteny plot in C using GD library
streak
for a 2d matrix (such as image) looks for islands to connected features. In black and white image matrix, will count the number of (black) islands using recursive algorithm
streakupd/ - this version saves the data to file for really huge 2d matrices.