aSPU (version 1.50)

MTaSPUsSetPath: Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.

Description

It gives p-values of the MTSPUsSetPath tests and MTaSPUsSetPath test with GWAS summary statistics.

Usage

MTaSPUsSetPath(
  Zs,
  corPhe,
  corSNP,
  pow1 = c(1, 2, 4, 8),
  pow2 = c(1, 2, 4, 8),
  pow3 = c(1, 2, 4, 8),
  snp.info,
  gene.info,
  n.perm = 1000,
  Ps = FALSE,
  prune = TRUE
)

Arguments

Zs

Z-score matrix. row represent SNPs and column represent traits. It could be P-values if the Ps option is TRUE.

corPhe

Correlation matirx of phenotypes to be tested; Estimated from Z-scores.

corSNP

Correlation matirx of the SNPs to be tested; estimated from a reference panel (based on the same set of the reference alleles as used in calculating Z-scores).

pow1

SNP specific power(gamma values) used in MTSPUsSetPath test.

pow2

GENE specific power(gamma values) used in MTSPUsSetPath test.

pow3

Trait specific power(gamma values) used in MTSPUsSetPath test.

snp.info

SNP information matrix, the 1st column is SNP id, 2nd column is chromosome #, 3rd column indicates SNP location.

gene.info

GENE information matrix, The 1st column is GENE id, 2nd column is chromosome #, 3rd and 4th column indicate start and end positions of the gene.

n.perm

number of permutations.

Ps

TRUE if input is p-value, FALSE if input is Z-scores. The default is FALSE.

prune

if it is TRUE, do pruing before the test using pruneSNP function.

Value

P-values for MTSPUsSetpath tests and MTaSPUsSetpPath test.

References

Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics, 33(1), 64-71

See Also

MTaSPUsSet

Examples

# NOT RUN {
Zs <- cbind ( c( 0.3, 0.2, 0.1,0.5,1.2),
          c(-.1, .3,-.1,.1,1.2) )

varSNP = cbind( c( 1, .1,0, 0, .11),
               c(.1,1, 0, 0, 0),
               c(0,0, 1, 0, 0),
               c(0,0, 0, 1, 0),
               c(.11,0,0,0,1) )

varPhe = cbind( c( 1, -.1),
               c(-.1,1) )

gene.info = data.frame( Gnm = c( "G1", "G2"), chr = c(1,3),
                    loc1 = c(0, 0), loc2 = c(10,10) )
snp.info = data.frame( rsid = c("rs1", "rs2", "rs3", "rs4", "rs5"),
                chr = c(1,1,3,3,3), loc = c(1,2,1,2,3) )
 out <- MTaSPUsSetPath(Zs, corPhe = varPhe, corSNP=varSNP,
            n.perm = 100, snp.info = snp.info, gene.info = gene.info)
out

# }