Noi/NOTES/2013-3-26: Difference between revisions
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>Noi (Created page with "== mQTL analysis on 5M SNPs (UCLA data set) == * Actually I finished analysis on these SNPs already, but there were some job exceed the limited walltime and got killed. I repe...") |
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- Copy all output onto genome-miner: /home/nplongth/Noi_scratch/DataAnalysis_2013/UCLA_mQTL_5MSNPs_repeat_20130326 | - Copy all output onto genome-miner: /home/nplongth/Noi_scratch/DataAnalysis_2013/UCLA_mQTL_5MSNPs_repeat_20130326 | ||
- Printout all output and sort out p-value | - Printout all output and sort out p-value | ||
cat mQTL-maf0.1.xa* | cat mQTL-maf0.1.xa* > all.mQTL-maf0.1.output (445603530) | ||
- To reduce sorting time, I print out only minimum p-value 0.05 for multiple testing correction (the result will be the same | |||
since the number of test will be specified in length parameter (n) in the R script. | |||
awk '{if($7<=0.05) print $0}' all.mQTL-maf0.1.output | sort -g -k7 > sorted.mQTL-maf0.1.minp0.05 | |||
'''BH.correction.R''' | |||
source("http://bioconductor.org/biocLite.R") | |||
biocLite("multtest") | |||
library(multtest) | |||
A=read.table("sorted.mQTL-maf0.1.minp0.05") | |||
B=A$V7 | |||
p_adj=p.adjust(B, method = "BH", n=445603530) | |||
dat <- cbind(A, p_adj) | |||
write.table(dat, file="BH.mQTL-maf0.1.minp0.05.output", sep="\t",append=F, row.names=FALSE, col.names=FALSE) |
Revision as of 21:21, 26 March 2013
mQTL analysis on 5M SNPs (UCLA data set)
- Actually I finished analysis on these SNPs already, but there were some job exceed the limited walltime and got killed. I repeat analysis again by splitting methylFreq to be smaller (3000 CpGs/job)
- Working directory on Triton cluster: /oasis/triton/scratch/nplongthongkum/20130219_UCLA_SZ_mQTL/20130324_mQTL_5M.SNPs_maf0.1_repeat
- Data summary
- Total tested CpGs: 76,408 autosomal CpGs
- Total tested SNPs: 5,257,772 SNPs
- Total number of tests: 445,603,530
- Copy all output onto genome-miner: /home/nplongth/Noi_scratch/DataAnalysis_2013/UCLA_mQTL_5MSNPs_repeat_20130326 - Printout all output and sort out p-value cat mQTL-maf0.1.xa* > all.mQTL-maf0.1.output (445603530) - To reduce sorting time, I print out only minimum p-value 0.05 for multiple testing correction (the result will be the same since the number of test will be specified in length parameter (n) in the R script. awk '{if($7<=0.05) print $0}' all.mQTL-maf0.1.output | sort -g -k7 > sorted.mQTL-maf0.1.minp0.05
BH.correction.R source("http://bioconductor.org/biocLite.R") biocLite("multtest") library(multtest) A=read.table("sorted.mQTL-maf0.1.minp0.05") B=A$V7 p_adj=p.adjust(B, method = "BH", n=445603530) dat <- cbind(A, p_adj) write.table(dat, file="BH.mQTL-maf0.1.minp0.05.output", sep="\t",append=F, row.names=FALSE, col.names=FALSE)