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Last data update: 2014.03.03

R: Creating a new CDF

prepareMaskedAffybatch

R Documentation

Creating a new CDF

Description

Create a new affyBatch, withprobes and probesetsdefined by mask.

Usage

prepareMaskedAffybatch(affy,cdfTablePath,exmask="none",cdfName="new_cdf",exclude=NA,cutoff=0.2)

Arguments

`affy`	An object of class `AffyBatch`.
`cdfTablePath`	Location of the probe information table. This is a plain text file with probes to build new cdf. It should contain 3 or 5 columns. Column 1: Probeset ID. Column 2: probe x-coordinate. Column 3: probes y-coordinate. Optional column 4: Mismatch probe x-coordinate. Optional column 5: Mismatch probe y coordinate.
`exmask`	Data frame with probe information, for example first element of the output of function `mask`. Should contain: column 1: probe x-coordinate, column 2:probe y coordinate, column 3 :probeset, column 4: quality score: values to based filtering on, probes with values smaller than cutoff are discarded.
`cdfName`	Name for the new CDF.
`cutoff`	With `mask.object`, defines the minimum quality score necessary for a probe to qualify to the new cdf.
`exclude`	Default 'NA'. If exclude set to a number>0, probesets with less than 'exclude' probes remaining after masking are excluded from the new affyBatch object.

Details

The function prepareMaskedAffybatch creates a new affyBatch including only the probes remaining after masking. Set of probes might be defined by a txt file, with cdfTablePath argument, or by a data frame mask.object and cutoff the probes have to exceed to be used in the new cdf.

Value

newAffyBatch

A list with an affyBatch object and an environment for the new CDF identifier.

Author(s)

Michael Lachmann, Mehmet Somel, Michael Dannemann, Anna Lorenc

References

Dannemann et al, The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 2009

Examples

## prepare new affy batch after masking
## using the expression mask object from the example of the mask function
data(AffyBatch)
data(exmask)
## AffyBatch object before masking
newAffyBatch
affyBatchAfterMasking <-
   prepareMaskedAffybatch(affy=newAffyBatch,exmask=exmask$probes)
## AffyBatch object after masking
affyBatchAfterMasking

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(maskBAD)
Loading required package: gcrma
Loading required package: affy
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maskBAD/prepareMaskedAffybatch.Rd_%03d_medium.png", width=480, height=480)
> ### Name: prepareMaskedAffybatch
> ### Title: Creating a new CDF
> ### Aliases: prepareMaskedAffybatch
> ### Keywords: internal
> 
> ### ** Examples
> 
> ## prepare new affy batch after masking
> ## using the expression mask object from the example of the mask function
> data(AffyBatch)
> data(exmask)
> ## AffyBatch object before masking
> newAffyBatch
AffyBatch object
size of arrays=640x640 features (22 kb)
cdf=newCdf (100 affyids)
number of samples=20
number of genes=100
annotation=hgu95av2
notes=
> affyBatchAfterMasking <-
+    prepareMaskedAffybatch(affy=newAffyBatch,exmask=exmask$probes)
Inferring mismatch positions from perfect match
Renaming columns:  probeset x y as probeset px py 
Regular run: more than  NA  probe per grouping
Made list.
Making env
finished making CDF!
> ## AffyBatch object after masking
> affyBatchAfterMasking
$newAffyBatch
AffyBatch object
size of arrays=640x640 features (22 kb)
cdf=new_cdf (100 affyids)
number of samples=20
number of genes=100
annotation=hgu95av2
notes=

$newCdf
<environment: 0x735a228>

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>