PhD Thesis

This algorithm was developed during the course of my PhD thesis project. An electronic version of my thesis can be found in the VUW Research Archive.

Sub-sampling analysis script

The custom R code used to carry out bootstrap sub-sampling analysis can be found here. To reduce loading time, the best/worst ranking can be calculated initially in the shell:

Report best/worst rank for each marker

x=bootstrap100_PP_males_anzgene_plink100_Aus_NZ.csv; pv ${x} | sort -t',' -k 2,2n -k 3,3rn | perl -F',' -lane 'if($run != $F[1]){$run = $F[1]; $rank=1; $lastVal=0; $lastRank=0} if($F[1] ne ""){$nextVal = $F[2]; $F[2] = ($F[2] == $lastVal) ? $lastRank : $rank; $lastRank = $F[2]; $lastVal = $nextVal; $rank++} print join(",",@F)' | sort -t',' -k 1,1 -k 3,3n | ~/scripts/ | gzip > maxminRank_${x}.gz;

Shell script explanation:

  1. Sort by bootstrap sub-sample then by calculated statistic in reverse numerical order
  2. Convert statistics to ranks, allowing ties
  3. Sort by marker, then by rank
  4. Preserve maximum and minimum ranks for each marker

Result graphing

The custom R code used to generate graphs for the poster can be found here. Two paths for generating a common intermediate data structure are provided in the code: one which loads directly the bootstrap script output and carries out ranking by R code, and another that uses the intermediate output files by the shell commands shown above.

Type 1 Diabetes

1000 Genomes, Chromosome 6 Subset

Parkinson's Disease

Multiple Sclerosis (not on poster)