Flush-methods {FLUSH.LVS.bundle} | R Documentation |
Perform filetring algorithm on an object of class exprSet or matrix, returning a subsetted object.
## 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,...)
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. |
An object of class FLUSH or ExpressionSet (if onlyExprs=TRUE).
Stefano Calza <calza@med.unibs.it>
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
## 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)