The CNVRs for LD b/w intensities & SNPs

The files used were:

% ll /nfs/team29/io1/data/ldapp/???_CNVs_with_freq_gt_2.txt

 2345 /nfs/team29/io1/data/ldapp/CEU_CNVs_with_freq_gt_2.txt

 2958 /nfs/team29/io1/data/ldapp/YRI_CNVs_with_freq_gt_2.txt

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LD Analysis Update

Plugged-in the refactored Rsquare Diff code (should name this R2D) into the LD Analysis pipeline. Am getting results but they look a bit strange. Briefly looking over the results indicates that I do not get the same results that I had before for a sample CNV. Need to verify this against Matt's example.

Trying again ...

Now trying out the corrections again using HighestLD v1.091390 as follows:


perl -IHighestLD-1.091390/lib highest_ld_v0.0.3.pl --configfile config.yml --input_file Affy6_22.txt.linear.txt --output_file Affy6_22.R2D --error_file Affy6_22_ERR.yml


Found the bug!

Turns out I was just being stupid (as usual)! In my attempts to make my code saner I used CSV instead of TSV files as my default. However, I forgot to set the format of my CNV resourse file to CSV as well. Hence I was not finding any values for my CNVs resulting in the undefined value bug.

Still need to find bug in LD analysis

I am yet to figure out why my refactored HighestLD.pm does not work as it should. As I am feeling a bit switched off now I will attack this when I get home and first thing tomorrow.

Results of the highest LD Analysis

The results of the LD Analysis on the intensity data are currently here:


/lustre/scratch1/sanger/io1/2009-05-06_LD_agillent-CNVs_HapMap-PhaseII-SNPs/CEU-intensity/results.csv
/lustre/scratch1/sanger/io1/2009-05-06_LD_agillent-CNVs_HapMap-PhaseII-SNPs/YRI-intensity/results.csv


The results for the genotype data are here:


/lustre/scratch1/sanger/io1/LD_Analysis/2009-05-07_rerun/ceu/genotype/results.csv
/lustre/scratch1/sanger/io1/LD_Analysis/2009-05-07_rerun/yri/genotype/results.csv