h.summary: Summary results from subset-search.

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

Description

This function produces summary results from subset-based association analysis.

Usage

h.summary(rlist, level = 0.05, digits = 3)

Arguments

rlist	List returned by h.traits or h.types
level	Level for confidence intervals. Default is 0.05 for 95% confidence intervals. The confidence intervals are obtained by inverting the corresponding multiple-testing adjusted p-values.
digits	Number of significant digits to retain in odds ratios and confidence intervals in the summary table

Details

Returns a list of data frames containing p-values, odds-ratios, confidence intervals and the traits/types for each analysis. The number of data frames in the list will depend on which function (h.traits or h.types) was called and on the function options specified.

Value

A list of data frames, one for each of the methods specified the original call of the functions h.traits or h.types. Each row of a data frame corresponds to a SNP and the values include p-values for overall association (including component-wise p-values for two-sided search), names of phenotypes or disease subtypes included in the best-subset, summary regression coefficients (e.g. log-odds-ratio for case-control studies) representing strength of association of a SNP with the identified subset of traits/subtype and corresponding confidence intervals.

See Also

h.forestPlot, h.traits, h.types

Examples

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

 # 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.