fm2: Output from FLASHFMwithFINEMAP for two simulated traits
In jennasimit/flashfm: flexible and shared information fine-mapping
fm2 R Documentation
Output from FLASHFMwithFINEMAP for two simulated traits
Description
Simulated data was generated using the mvrnorm function in R and genotype matrix X. The two traits have correlation 0.4 and
each has two causal variants, of which one, rs61839660 is shared between traits; trait 1 has second
causal variant rs62626317 and trait 2 has second causal variant rs11594656. The traits are from a sample
of 2000, with no missing measurements.
Usage
fm2
Format
An object of class list of length 2.
Details
fm2 was generated using the following command, where all called objects exist in the flashfm package,
fstub is a file prefix for FINEMAP input/output files, and FMpath is the path to the software FINEMAP
fm2 <- FLASHFMwithFINEMAP(gwas.list,corX,raf,ybar,N,fstub="DIRresults/eg",TOdds=1,covY,cpp=.99,NCORES=2,FMpath="/software/finemap_v1.4_x86_64/finemap_v1.4_x86_64")
JAMexpanded.multi(beta,X,snpinfo,ybar,diag(covY),N,chr=10,fstub=fstub,mafthr=0.005,path2plink="/software/plink",r2=0.99,save.path=fstubJ,related=FALSE,y=NULL)
jennasimit/flashfm documentation built on July 31, 2022, 7:32 p.m.
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| fm2 | R Documentation |
Output from FLASHFMwithFINEMAP for two simulated traits
Description
Simulated data was generated using the mvrnorm function in R and genotype matrix X. The two traits have correlation 0.4 and each has two causal variants, of which one, rs61839660 is shared between traits; trait 1 has second causal variant rs62626317 and trait 2 has second causal variant rs11594656. The traits are from a sample of 2000, with no missing measurements.
Usage
fm2
Format
An object of class list of length 2.
Details
fm2 was generated using the following command, where all called objects exist in the flashfm package, fstub is a file prefix for FINEMAP input/output files, and FMpath is the path to the software FINEMAP fm2 <- FLASHFMwithFINEMAP(gwas.list,corX,raf,ybar,N,fstub="DIRresults/eg",TOdds=1,covY,cpp=.99,NCORES=2,FMpath="/software/finemap_v1.4_x86_64/finemap_v1.4_x86_64") JAMexpanded.multi(beta,X,snpinfo,ybar,diag(covY),N,chr=10,fstub=fstub,mafthr=0.005,path2plink="/software/plink",r2=0.99,save.path=fstubJ,related=FALSE,y=NULL)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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