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whradjbmi.giant-ukbb.meta.ecf
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######### Load in the data, rename columns where relevant, merge in reference data (chr, pos, a1, a2) and align alleles across files
#########
DEFINE --strMissing NA
--strSeparator WHITESPACE
--acolIn SNP;Allele1;Allele2;Freq1;Effect;StdErr;P.value;Direction;Nmeta;Info
--acolInClasses character;character;character;numeric;numeric;numeric;numeric;character;numeric;character
--acolNewName SNP;A1;A2;frqA1;beta;se;pval;dir;nmeta;info
--pathOut ./
EASYIN --fileIn /path/to/meta-analysis/metal/whradjbmi/combined/fat-distn.giant.ukbb.meta-analysis.whradjbmi.combined.annotated.tbl.gz
--fileInShortName whradjbmi.combined
--fileInTag whradjbmi.combined
EASYIN --fileIn /path/to/meta-analysis/metal/whradjbmi/females/fat-distn.giant.ukbb.meta-analysis.whradjbmi.females.annotated.tbl.gz
--fileInShortName whradjbmi.females
--fileInTag whradjbmi.females
EASYIN --fileIn /path/to/meta-analysis/metal/whradjbmi/males/fat-distn.giant.ukbb.meta-analysis.whradjbmi.males.annotated.tbl.gz
--fileInShortName whradjbmi.males
--fileInTag whradjbmi.males
########
########
START EASYX
## Merge together the data
MERGE --colInMarker SNP
--fileRef ./ref.data.chr.pos.giant-ukbb.txt.gz
--strMissing NA StrSeparator SPACE
--colRefMarker SNP
--strRefSuffix .ref
--blnWriteNotInRef 0
--blnWriteNotInIn 0
--strTag REF
MERGEEASYIN --colInMarker SNP --blnMergeAll 0
## align the alleles to keep things easy
ADJUSTALLELES --colInA1 A1.whradjbmi.males
--colInA2 A2.whradjbmi.males
--colInFreq frqA1.whradjbmi.males
--colInBeta beta.whradjbmi.males
--colRefA1 A1.whradjbmi.females
--colRefA2 A2.whradjbmi.females
## plot the Manhattan plot
MHPLOT --colMHPlot pval.whradjbmi.combined
--colInChr Chr.ref.whradjbmi.combined
--colInPos Pos.ref.whradjbmi.combined
--astrDefaultColourChr azure3;grey85
--numPvalOffset 0.05
--blnYAxisBreak 1
--numYAxisBreak 30
--anumAddPvalLine 5e-8;5e-9
--astrAddPvalLineCol grey30;grey50
--anumAddPvalLineLty 6;6
--strFormat png
--fileAnnot ./annotate.whradjbmi.combined.index.snps.gcta.cojo-slct.lst
--numAnnotPvalLim 5e-9
--numAnnotPosLim 50000
## create a Miami plot
MIAMIPLOT --colMIAMIPlotUp pval.whradjbmi.females
--colMIAMIPlotDown pval.whradjbmi.males
--colInChr Chr.ref.whradjbmi.combined
--colInPos Pos.ref.whradjbmi.combined
--astrDefaultColourChrUp royalblue1;royalblue3
--astrDefaultColourChrDown coral3;coral1
--numPvalOffset 0.05
--blnYAxisBreak 1
--numYAxisBreak 30
--anumAddPvalLine 5e-8;5e-9
--astrAddPvalLineCol grey30;grey50
--anumAddPvalLineLty 6;6
--strFormat png
--fileAnnot ./annotate.whradjbmi.females.males.index.snps.gcta.cojo-slct.lst
--numAnnotPvalLim 5e-9
--numAnnotPosLim 50000
## QQ plot, stratified by sex
QQPLOT --acolQQPlot pval.whradjbmi.females;pval.whradjbmi.males
--astrColour royalblue1;coral1
--anumSymbol 0;1
--anumCex 1.5;1.5
--numPvalOffset 0.05
## QQ plot, combined analysis
QQPLOT --acolQQPlot pval.whradjbmi.combined
--astrColour azure3
--anumSymbol 0
--anumCex 1.5
--numPvalOffset 0.05
## run the test for sexual dimorphism
CALCPDIFF --acolBETAs beta.whradjbmi.males;beta.whradjbmi.females
--acolSEs se.whradjbmi.males;se.whradjbmi.females
--colOutPdiff psexdiff
--blnCovCorrection 0
## extract a list of important SNPs
EXTRACTSNPS --colInMarker SNP
--fileRef ./whradjbmi.all-signal-snps.toExtract.lst
--colRefMarker SNP
--strTag indexSnps
STOP EASYX