Editing
Dinh 2011/NOTES/2011-11-18
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
==Age-related Macular Degeneration (AMD) [Kang Zhang lab collaboration]== * I did the mQTL on the 30 samples which we have genotyping array data for (geno_GA.txt) * Also SOM analysis on these 30 samples * All 30 are diseased patients ... Not useful for finding bio-markers ===Generating tped and tfam and methylation matrix files=== *TFAM awk '{print $2}' geno_GA.txt | sort -u > geno_GA.tfam (removed unwanted lines first) awk '{print sum" "$2" 0 0 0 -9"; sum++}' geno_GA.tfam > tmp vim tmp # add in number 30 for the first row. sort -k1,1n tmp > geno_GA.tfam *getChrPos.pl for rs sites ./getChrPos.pl geno_GA.txt < ../HsRef/Hg19/snp134_snv.txt > annotated.geno_GA.txt & *getTPED_11172011.pl ./getTPED_11172011.pl geno_GA.tfam < annotated.geno_GA.txt > geno_GA.tped & *Modified allBED2Matrix to get methylation matrix: The script was modified to read only 30 specified samples nohup ./allBED2Matrix.pl AMD-BED 27 1 0.1 > geno_GA_30.methylMatrix_min27_std0.1 & *Split CpGs file and run mQTL: split -l 10000 geno_GA_30* geno_methylMatrix_frag head -1 geno_GA_30* > header for f in geno_methylMatrix_frag* do cat header $f > tmp ./createPhenoFile.pl geno_GA.tfam tmp > $f done; mkdir phenoAB mkdir phenoAC mkdir phenoAD mkdir phenoAE mkdir phenoAF mkdir phenoAG mkdir phenoAH mkdir phenoAI mkdir phenoAJ mkdir phenoAK mkdir phenoAL mkdir phenoAM mv geno_methylMatrix_fragaa phenoAA/matrix.txt mv geno_methylMatrix_fragab phenoAB/matrix.txt mv geno_methylMatrix_fragac phenoAC/matrix.txt mv geno_methylMatrix_fragad phenoAD/matrix.txt mv geno_methylMatrix_fragae phenoAE/matrix.txt mv geno_methylMatrix_fragaf phenoAF/matrix.txt mv geno_methylMatrix_fragag phenoAG/matrix.txt mv geno_methylMatrix_fragah phenoAH/matrix.txt mv geno_methylMatrix_fragai phenoAI/matrix.txt mv geno_methylMatrix_fragaj phenoAJ/matrix.txt mv geno_methylMatrix_fragak phenoAK/matrix.txt mv geno_methylMatrix_fragal phenoAL/matrix.txt mv geno_methylMatrix_fragam phenoAM/matrix.txt for f in phenoA* do cd $f /media/2TB_store2/Dinh_Scratch/scripts/mQTL_2MB_plink.pl ../geno_GA matrix.txt > results.txt & cd .. done; *'''I still need to process the result files''' *Since this analysis was done on all GA (disease status samples), it might not be worthwhile to continue looking at this. ===R package oposSOM analysis=== * Wirth, Loeffler, v.Bergen, Binder: Expression cartography of human tissues using self organizing maps. (BMC Bioinformatics 2011) library(oposSOM) A = read.table("geno_GA_30.methylMatrix_min27_std0.1", header=TRUE, row.name=1) A$STDEV=NULL A$min_RD=NULL A$mean_RD=NULL B = as.matrix(A) run.pipeline(B, dataset.name="AMD_std0.1_30", dim.som1=20, dim.som2=20) *Understanding the dim.som1 and dim.som2 **dim.som1 = size of the primary SOM / resolution of the expression profiles: number of tiles equals dim.som1^2. **dim.som2 = resolution of the second level SOM: number of tiles equals dim.som2^2 *Since the analysis doesn't allow for missing values, can we iteratively switch out samples to find a converging best minimal set? **To allow for ~4% missing values, I can switch out 2 samples in control and in GA at each iteration. **The number of ways 2 samples could be selected out of 48: 48!/(48-2)! = 2256. Since, there are control and GA, = 2256^2 = 5,089,536 **Do 1 million random permutation to sample 20% of the solution space? But since we only allow for 4% missing values, there should be very little variations between the solutions. But with probe capture, we only get around 80-90% sites shared between two samples. **Lets try permuting two solutions each, from 35+35, 37+37, 39+39, 41+41, 43+43, 45+45, 47+47 to see how much overlaps are there between two sets.
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information