promise.genestat: Function to Calculate PROMISE Statistics

In PROMISE: PRojection Onto the Most Interesting Statistical Evidence

Description

a function to calculate individual gene and PROMISE statistics for a defined pattern of association

Usage

promise.genestat(Y, ph.data, ph.pattern, strat = NULL, proj0=FALSE)

Arguments

Y	a data frame with row corresponding to probe set and column corresponding to subjects, the order of column should match order of row in ph.data.
ph.data	a data frame with rows corresponding to subjects and columns corresponding to endpoint variables.
ph.pattern	a data frame with column headers: stat.coef, stat.func, endpt.vars. The stat.coeff column gives the coefficients for combining the statistics of association of genomic variable with individual endpoint variable into the ultimate PROMISE statistic. If proj0=TRUE, the stat.coeff is ignored. The stat.func column gives the name of the R routine that computes the test statistic of association of the end point variables. jung.rstat and spearman.rstat are provided. Users can provide their own routines accordingly. The endpt.vars column gives the name(s) of variable(s) in ph.data needed to compute each term of the PROMISE statistic. A comma without a space should be used to separate multiple variables that correspond to the same term in the association pattern definition.
strat	a vector of stratum to calculate stratified statistics. The default is NULL.
proj0	indicator of whether projection to 0 is performed. It takes two valid values: TRUE or FALSE. If proj0=TRUE, PROMISE statistics is the sum of squares of individual statitics. The default is FALSE.

Value

a matrix of statistics. Each row gives gene's statistics of each individual endpoint and the PROMISE statistics defined in ph.pattern.

Note

a function internally called by PROMISE.

Author(s)

Stan Pounds [e-mail]; Xueyuan Cao [e-mail]

References

Pounds S, Cheng C, Cao X, Crews KR, Plunkett W, Gandhi V, Rubnitz J, Ribeiro RC, Downing JR, and Lamba J (2009) PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables. Bioinformatics 25: 2013-2019

See Also

PROMISE

Examples

## load sampExprSet, phPatt.
data(sampExprSet)
data(phPatt)

Y <- exprs(sampExprSet)
ph.data <- pData(phenoData(sampExprSet))

test <- promise.genestat(Y, ph.data, phPatt, strat=ph.data[, 5])
test2 <- promise.genestat(Y, ph.data, phPatt, strat=ph.data[, 5], proj0=TRUE)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode

PROMISE documentation built on Nov. 8, 2020, 5:15 p.m.