buildPatterns: Build a matrix with all possible patterns given a number of...

In gaga: GaGa hierarchical model for high-throughput data analysis

Description

Creates a matrix indicating which groups are put together under each pattern. The number of possible patterns increases very fast as the number of groups increases. This function provides an easy way to compute all possible patterns. The output of this function is usually used for the patterns parameter of the lmFit function.

Usage

buildPatterns(groups)

Arguments

groups

Character containing the names of the groups at which samples may belong to. If the output of the function is going to be used in fitGG it must match the group levels specified in the groups parameter that will be given to fitGG.

Examples

buildPatterns(groups=c('GroupControl','GroupA','GroupB'))

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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: coda
Loading required package: EBarrays
Loading required package: lattice
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
     GroupA GroupB GroupControl
[1,]      0      0            0
[2,]      0      0            1
[3,]      0      1            0
[4,]      0      1            1
[5,]      0      1            2

gaga documentation built on Nov. 8, 2020, 5:49 p.m.