h.traits: Heterogeneous traits or studies

In ASSET: An R package for subset-based association analysis of heterogeneous traits and subtypes

Description

Performs one-sided or two-sided subset-based meta-analysis of heteregeneous studies/traits.

Usage

h.traits(snp.vars, traits.lab, beta.hat, sigma.hat, ncase, ncntl, 
  cor=NULL, cor.numr=FALSE, search=NULL, side=2, meta=FALSE, 
  zmax.args=NULL, meth.pval=c("DLM","IS","B"), pval.args=NULL)

Arguments

snp.vars	A character vector giving the SNP names to be analyzed. No default.
traits.lab	A character vector giving the names/identifiers of the k studies/traits being analyzed. The order of this vector must match the columns of beta.hat and sigma.hat No default.
beta.hat	A matrix of dimension length(snp.vars) by (k) (or a vector of length k when 1 SNP is passed). Each row gives the coefficients obtained from the analysis of that SNP across the k studies/traits. No default.
sigma.hat	A vector or matrix of same dimension as beta.hat, giving the corresponding standard errors. No default.
ncase	The number of cases in each of the k studies. This can be same for each SNP, in which case ncase is a vector of length k. Alternatively if the number of non-missing cases analyzed for each SNP is known, ncase can be a length(snp.vars) by (k) matrix. No default.
ncntl	Same as ncase (above) for controls. No default.
cor	Either a k by k matrix of inter-study correlations or a list containing three case/control overlap matrices (for case-control studies) named N11, N00 and N10. See details. Default is NULL, so that studies are assumed to be independent. The rows and columns of all matrices needs to be in the same order as traits.lab and columns of beta.hat and sigma.hat
cor.numr	Logical. When specified as TRUE the correlation information is used for optimal weighting of the studies in the definition of the meta-analysis test-statistics. The default is FALSE. In either case, the correlation is accounted for variance calculation of the meta-analysis test-statistic.
search	1, 2 or NULL. Search option 1 and 2 indicate one-sided and two-sided subset-searches respectively. The default option is NULL that automatically returns both one-sided and two-sided subset searches. Default is NULL.
side	Either 1 or 2. For two-tailed tests (where absolute values of Z-scores are maximized), side should be 2. For one-tailed tests, side should be 1 (positive tail is assumed). Default is 2. The option is ignored when search=2 since the two-sided subset search is automatically a two-sided test.
meta	Logical. When specified as TRUE, standard fixed effect meta-analysis results are returned together with results from subset-based meta-analysis. The Default is FALSE.
zmax.args	Optional arguments to be passed to z.max as a named list. This option can be useful if the user wants to restrict subset searches in some structured way, for example, incorporating some ordering constraints.
pval.args	Optional arguments to be passed to p.dlm or p.tube as a named list. This option can be useful if the user wants to restrict subset searches in some structured way, for example, incorporating some ordering constraints.
meth.pval	The method of p-value computation. Currently the options are DLM (Discrete Local Maximum), IS(Exact Importance Sampling) and B (Bonferroni) with the default option being DLM. The IS method is currently computationally feasible for analysis of at most k=10 studies/traits

Details

The one-sided subset search maximizes the standard fixed-effect meta-analysis test-statistics over all possible subsets (or over a restricted set of subsets if such an option is specified) of studies to detect the best possible association signals. The p-value returned for the maximum test-statistics automatically accounts for multiple testing penalty due to subset search and can be taken as an evidence of an overall association for the SNP accross the k studies/traits. The one-sided method automatically guarantees identification of studies/traits that have associations in the same direction and thus is useful in applications where it is desirable to identify SNPs that shows effects in the same direction across multiple traits/studies. The two-sided subset search, applies one-side subset search separately for positively and negatively associated traits for a given SNP and then combines the association signals from two directions into a single combined chi-square type statistic. The method is sensitive in detecting SNPs that may be associated with different traits in different directions.

The methods allow for accounting for correlation among studies/subject that might arise due to shared subjects across distinct studies or due to correlation among related traits in the same study. For application of the method for meta-analysis of case-control studies, the matrices N11, N10 and N00 denote the number subjects that are shared between studies by case-control status. By defintion, the diagonals of the matrices N11 and N00 contain the number of cases and controls, respectively, in the k studies. Also, by definition, the diagonal of N10 is zero since cases cannot serve as controls and vice versa in the same study. The most common situation may involve shared controls accross studies, ie non-zero off-diagonal elements of the matrix N00.

The output standard errors are approximate (based on inverting p-values) and are used for constructing confidence intervals in h.summary and h.forestPlot.

Value

A list containing 3 main component lists named:

(1) "Meta" (Results from standard fixed effect meta-analysis of all studies/traits). This list is non-null when meta is TRUE and contains 3 vectors named (pval, beta, sd) of length same as snp.vars.

(2) "Subset.1sided" (one-sided subset search): This list is non-null when search is NULL or 1 and contains, 4 vectors named (pval, beta, sd, sd.meta) of length same as snp.vars and a logical matrix named "pheno" with one row for each snp and one column for each phenotype. For a particular SNP and phenotype, the entry has "TRUE" if this phenotype was in the selected subset for that SNP. In the output, the p-value is automatically adjusted for multiple testing due to subset search. The beta and sd correspond to the standard fixed-effect meta-analysis estimate and corresponding standard error estimate for the regression coefficient of a SNP based only on those studies/traits that are included in the identified subset. The vector sd.meta gives the meta-analysis standard errors for estimates of beta based on studies in the identified subset ignoring the randomness of the subset.

(3) Subset.2sided (two-sided subset search) This list is non-null when search is NULL or 2 and contains 9 vectors named (pval, pval.1, pval.2, beta.1, sd.1, beta.2, sd.2, sd.1.meta, sd.2.meta) of length same as snp.vars and two matrices named "pheno.1" and "pheno.2" giving logical indicators of a phenotype being among the positively or negatively associated subsets (respectively) as identified by 2-sided subset search. In the output, while pval provides the significance of the overall test-statistics that combined association signals from two directions, pval.1 and and pval.2 return the corresponding level of significance for each of the component one-sided test-statistics in the positive and negative directions. The values (beta.1, sd.1, beta.2, sd.2) denote the corresponding meta-analysis estimate of regression coefficients and standard errors for the identifed subsets of traits/studies that show association in positive and negative directions, respectively. The vector sd.1.meta and sd.2.meta give the meta-analysis standard errors for estimates of beta based on studies in the identified subset ignoring the randomness of the subset in positive and negative directions, respectively.

The other objects in the list are the input arguments passed into h.traits.

References

Samsiddhi Bhattacharjee, Preetha Rajaraman, Kevin B. Jacobs, William A. Wheeler, Beatrice S. Melin, Patricia Hartge, GliomaScan Consortium, Meredith Yeager, Charles C. Chung, Stephen J. Chanock, Nilanjan Chatterjee. A subset-based approach improves power and interpretation for combined-analysis of genetic association studies of heterogeneous traits. Am J Hum Genet, 2012, 90(5):821-35

See Also

h.summary, h.forestPlot

Examples

 # Use the example data
 data(ex_trait, package="ASSET")

 # Display the data, and case/control overlap matrices
 data
 N00
 N11
 N10
 
 # Define the input arguments to h.traits
 snps       <- as.vector(data[, "SNP"])
 traits.lab <- paste("Trait_", 1:6, sep="")
 beta.hat   <- as.matrix(data[, paste(traits.lab, ".Beta", sep="")])
 sigma.hat  <- as.matrix(data[, paste(traits.lab, ".SE", sep="")])
 cor        <- list(N11=N11, N00=N00, N10=N10)
 ncase      <- diag(N11)
 ncntl      <- diag(N00)

 # Now let us call h.traits on these summary data. 
 res <- h.traits(snps, traits.lab, beta.hat, sigma.hat, ncase, ncntl, cor=cor, 
                 cor.numr=FALSE, search=NULL, side=2, meta=TRUE, 
                 zmax.args=NULL, meth.pval="DLM")
 
 h.summary(res)

ASSET documentation built on Nov. 8, 2020, 5:20 p.m.