Microarray probes filtering

Description

Function to filter microarray probes according to coefficient of variation

Usage

cv.filter(data, cutoff = 0.05)

Arguments

Value

Expression matrix, probes with CV below cutoff are filtered out.

Author(s)

Ivana Ihnatova

Examples

data(Singhdata)
data<-Singhdata$esets[[1]][1:1000,]
data.filtered<-cv.filter(data)
head(data.filtered)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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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/cv.filter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cv.filter
> ### Title: Microarray probes filtering
> ### Aliases: cv.filter
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(Singhdata)
> data<-Singhdata$esets[[1]][1:1000,]
> data.filtered<-cv.filter(data)
> head(data.filtered)
     Normal  Normal.1  Normal.2  Normal.3  Normal.4  Normal.5  Normal.6
3  3.783717  4.118151  4.216871  4.223820  4.364816  4.092585  3.999631
4  3.152045  3.633564  3.767186  3.901121  4.001623  3.851386  3.703695
5  5.452305  6.716646  6.431922  6.612021  6.348126  6.762278  6.582096
7  7.207633  5.287455  5.419958  5.413211  5.378318  5.330816  5.280372
8  3.077360  3.383413  3.646509  3.529396  3.436742  3.634367  3.428753
10 6.833431 11.661911 11.549448 11.347327 11.535383 12.120565 11.493540
    Normal.7  Normal.8  Normal.9   Tumour  Tumour.1  Tumour.2  Tumour.3
3   4.294531  4.254407  4.010793 3.693758  3.837384  3.939096  3.681716
4   3.771112  3.723193  3.507246 3.335860  3.448102  3.423283  3.193589
5   6.648011  6.512724  6.342057 5.623833  6.284547  6.348526  5.872347
7   5.449844  5.343616  5.037288 8.411844  5.092543  5.420076  5.999140
8   3.803338  3.486255  3.453213 3.349204  3.461864  3.514328  3.005631
10 11.950284 11.611832 11.228292 9.235940 11.559250 11.574905 10.786439
    Tumour.4  Tumour.5 Tumour.6  Tumour.7  Tumour.8  Tumour.9
3   3.947196  3.861054 3.635040  3.898488  4.311007  3.786629
4   3.536552  3.501316 3.238554  3.311750  3.591361  3.358651
5   6.204390  6.323174 5.756556  6.148963  6.439817  5.940263
7   5.197023  5.916329 8.696407  5.060513  5.389452  6.057525
8   3.287253  3.383124 3.125745  3.429256  3.685988  3.515686
10 11.249121 11.332153 8.763352 11.206492 11.524489 10.477612
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>