Flush-methods: Flush genes

In Senbee/FLUSH_LVS_bundle: FLUSH.LVS.bundle

Description

Perform filetring algorithm on an object of class exprSet or matrix, returning a subsetted object.

Usage

## S4 method for signature 'matrix'
Flush(object, RA, check = TRUE, ...)
## S4 method for signature 'ExpressionSet'
Flush(object, RA, check = TRUE, onlyExprs =
TRUE, which = 1)
## S4 method for signature 'ExpressionSet'
Flushit(object,RA, proportion=0.6, df=10, delta=NULL, lambda=NULL,
                              check = TRUE, onlyExprs=TRUE, which=1,...)

Arguments

object	An object of class exprSet or matrix
RA	An object of class RA as from compute.RA and optionally FlushSet
proportion	Proportion of genes to filter out, i.e. the quantile to estimate in the quantile regression. Used only if RA doesn't come from FlushSet
delta	Number. Weighting parameter. Used only if RA doesn't come from FlushSet
lambda	Number. Weighting parameter. Used only if RA doesn't come from FlushSet
df	Integer. Degrees of freedom of the B-spline. Used only if RA doesn't come from FlushSet
check	Logical. If TRUE some additional check on probes name consistency are performed.
onlyExprs	Logical. If TRUE returns an object of class ExpressionSet with the selected features. If FALSE an object of class FLUSH is returned with the RA object included (for plotting)
which	Integer. If more than one proportion is supplied, which one to use for filtering. Defaults to 1.
...	additional arguments.Not used.

Value

An object of class FLUSH or ExpressionSet (if onlyExprs=TRUE).

Author(s)

Stefano Calza <[e-mail]>

References

Stefano Calza, Wolfgang Raffelsberger, Alexander Ploner, Jose Sahel, Thierry Leveillard and Yudi Pawitan. Filtering genes to improve sensitivity in oligonucleotide microarray data analysis - 2007 NAR

See Also

RAplot, fitRA, FlushSet

Examples

## Not run: 
data(FLUSH.RData)

choe.RA <- compute.RA(choe)
choe.fSet <- FlushSet(choe.RA)
choe.Flush <- Flush(choe.MAS5,choe.fSet, onlyExprs = FALSE)
choe.Flush <- Flush(choe.MAS5,choe.choe.RA, proportion=0.6)

## End(Not run)

Senbee/FLUSH_LVS_bundle documentation built on May 9, 2019, 1:21 p.m.