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Tutorial: EMMAX GotCloud STOM (view source)

Revision as of 10:56, 6 January 2014

793 bytes removed ,  10:56, 6 January 2014
→‎Lecture 8 : Sequence-based association using EPACTS
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= STOM 2014 Workshop - Practical Sessions =
 
= STOM 2014 Workshop - Practical Sessions =
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Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow the [[ http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344 | link]]
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Welcome to Hyun Min Kang's practical session guide page for STOM 2014 workshop. If you do not know what STOM 2014 workshop is please follow http://bibs.snu.ac.kr/board/index.php?catid=201&bcid=344
    
This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.
 
This page is intended to supplement the slides presented in the practical sessions of STOM 2014 workshop by facilitating easy copy-and paste of commands illustrated in the example, in the case the speed of the lecture is too fast for you.
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Note that some commands can be very long and may go farther than the browser's width
 
Note that some commands can be very long and may go farther than the browser's width
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== Lecture 2 ==
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== Lecture 2 : Genomic Control, PCA, EMMAX ==
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* To see the files for the session, type
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_2 | Page for Practice 2 ]]
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ls /data/stom2014/session2/
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If you see any errors, please let me know now!
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* For convenience, let’s set some variables
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== Lecture 5 : GotCloud Alignment Pipeline ==
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  export S2=/data/stom2014/session2
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mkdir ~/out
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* Run naive association test using PLINK
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_5 | Page for Practice 5 ]]
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$S2/bin/plink --noweb --bfile $S2/data/1000G.auto.omni.phased.EUR --pheno $S2/data/1000G_EUR_20_1459060.phe --linear --out ~/out/naive
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== Lecture 6 : GotCloud Variant Calling Pipeline + samtools ==
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* Check your output file and see what it looks like
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_6 | Page for Practice 6 ]]
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less ~/out/naive.assoc.linear
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== Lecture 8 : Sequence-based association using EPACTS ==
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* Check the p-value at the causal variant
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Please see [[Tutorial:_EMMAX_GotCloud_STOM:_Lecture_8 | Page for Practice 8 ]]
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grep -w ADD ~/out/naive.assoc.linear | grep 20:1459060
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* Draw QQ plot using the following R commands
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> source('/data/stom2014/session2/r/qqconf.r')
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> T <- read.table('~/out/naive.assoc.linear',header=TRUE)
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> pdf('~/out/naive.pdf')
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> qq.conf.beta(T$P)
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> dev.off()
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* Add --adjust option to enable genomic control
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$S2/bin/plink --noweb --bfile $S2/data/1000G.auto.omni.phased.EUR --pheno $S2/data/1000G_EUR_20_1459060.phe --linear --adjust --out ~/out/naive
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* Calculate inflation factor on your own
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> T <- read.table('~/out/naive.assoc.linear',header=TRUE)
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** First, find the median p-value
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> median(T$P)
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> 0.4814
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** Convert p-value into chi-square using R, and compute lambda
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> qchisq(0.4814,1,lower.tail=FALSE)
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[1] 0,4956901
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> 0.4958032/0.456
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[1] 1.08704
 
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