makeSNPgroups2 | R Documentation |
Make two sets of SNP groups using fine-mapping information from all of the traits using two sets of results and maps the names between them
makeSNPgroups2( main.input, fm.multi, is.snpmat, min.mppi = 0.01, minsnpmppi = 0.001, r2.minmerge = 0.5 )
main.input |
output from flashfm.input function |
fm.multi |
output from flashfm function |
is.snpmat |
logical taking value TRUE when genotype matrix is provided and FALSE when covariance matrix is given |
min.mppi |
trim snp groups with total MPPI < min.mppi in all diseases; default 0.01 |
minsnpmppi |
only group snps with total MPPI > minsnpmppi; default 0.001 |
r2.minmerge |
merge groups with minimum between-group r2 > r2.minmerge; default 0.5 |
list of three objects: groups.fm is a list of SNP groups using the single-trait results; groups.flashfm is a list of SNP groups using the flashfm results; group.sizes is a table of SNP group sizes for the two sets of groups
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