Function to count soft pattern matches

Description

Funtion counts number of observed soft matches in meta-analysis

Usage

patternMatch(X.discret, unique.pat)

Arguments

Value

Numeric vector of number of soft pattern matches for each pattern.

Author(s)

Code provided by Xinan Yang <xnyang@seu.edu.cn>

References

Yang, X., Bentink, S. a Spang, R. 2005, Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities, Biomedical Microdevices, vol.7:3

Examples

A<-matrix(c(1,0,0,1,0,1,0,1,1,0,1,0,1,0,1), ncol=3, nrow=10)
uni<-c("011","101","110","111")
patternMatch(A,uni)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

The following object is masked from 'package:genefilter':

    rowVars

Loading required package: xtable
Loading required package: multtest
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

The following objects are masked from 'package:GeneMeta':

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/patternMatch.Rd_%03d_medium.png", width=480, height=480)
> ### Name: patternMatch
> ### Title: Function to count soft pattern matches
> ### Aliases: patternMatch
> ### Keywords: nonparametric
> 
> ### ** Examples
> 
> 
> A<-matrix(c(1,0,0,1,0,1,0,1,1,0,1,0,1,0,1), ncol=3, nrow=10)
> uni<-c("011","101","110","111")
> patternMatch(A,uni)
[1] 3 4 3 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>