Estimate the detectable probe ratio

Description

Estimate the detectable probe ratio of each probe, sample or just return an AP matrix

Usage

detectionCall(x.lumi, Th = 0.01, type = c('probe', 'sample', 'matrix'))

Arguments

Value

If the type is 'probe', then returns the presentCount of each probe. If the type is 'sample', then return the detectable probe ratio of each sample. If the type is 'matrix', then return the AP matrix, in which 'A' represents absent (the detect p-value less than threshold) and 'P' represents present.

Author(s)

Pan Du

See Also

lumiQ

Examples

## load example data
data(example.lumi)
## load example data
data(example.lumi)

## estimate the detect call (percentage of expressed genes) of each sample
temp <- detectionCall(example.lumi, type='sample')
print(temp)

## estimate the present count of each gene (probe)
temp <- detectionCall(example.lumi, type='probe')
hist(temp)

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.

R is a collaborative project with many contributors.
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.
Type 'q()' to quit R.

> library(lumi)
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, 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

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/detectionCall.Rd_%03d_medium.png", width=480, height=480)
> ### Name: detectionCall
> ### Title: Estimate the detectable probe ratio
> ### Aliases: detectionCall
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> ## load example data
> data(example.lumi)
> 
> ## estimate the detect call (percentage of expressed genes) of each sample
> temp <- detectionCall(example.lumi, type='sample')
> print(temp)
 A01  A02  B01  B02 
4310 4491 4559 4558 
attr(,"threshold")
[1] 0.01
> 
> ## estimate the present count of each gene (probe)
> temp <- detectionCall(example.lumi, type='probe')
> hist(temp)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>