Kun:LabNotes/CpgSeq/2011-10-14: Difference between revisions
Jump to navigation
Jump to search
m (Created page with '==Analysis of BSPP data from Geographic Astrophy (GA) patients== *96 blood samples from cases and controls were provided by Kang Zhang's group. *Noi performed the BSPP capture an…') |
|||
Line 5: | Line 5: | ||
Noi should fill in this part. | Noi should fill in this part. | ||
===Regression analysis=== | ===Regression analysis=== | ||
*The working directory is on genome-miner | |||
/home/kunzhang/mQTL/KangZhang_GA | |||
*One data set (2200001) was removed due to low capture efficiency and low sequencing depth. | *One data set (2200001) was removed due to low capture efficiency and low sequencing depth. | ||
*Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed): | *Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed): |
Revision as of 01:27, 15 October 2011
Analysis of BSPP data from Geographic Astrophy (GA) patients
- 96 blood samples from cases and controls were provided by Kang Zhang's group.
- Noi performed the BSPP capture and the sequencing was done in BioGem (110929_SN1001)
Summary statistics on sequencing, mapping and CpG methylation calling
Noi should fill in this part.
Regression analysis
- The working directory is on genome-miner
/home/kunzhang/mQTL/KangZhang_GA
- One data set (2200001) was removed due to low capture efficiency and low sequencing depth.
- Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed):
allBED2Matrix.pl BED 76 1 0.1 > KangZhang_GA_BSPP_95_methylationMatrix.txt &
- I ended up getting a matrix containing 136,417 variable CpG sites.
- I wrote a Perl Script to perform linear regression on five factors: disease status, sex, age, BMI, smoking: GA_methylation_regression.txt.
- Sites that might be significantly contributed by one of these factors were reported.
- I used a stringent cutoff of 3.5 for the t-statistics on reporting the data in individual files (allowed for more detailed analysis in R).
- The test statistics for all the tested sites were also reported in a separate file.