Description Usage Arguments Value Author(s) References See Also Examples
Perform filetring algorithm on an object of class exprSet or matrix, returning a subsetted object.
1 2 3 4 5 6 7 8 | ## 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
1 2 3 4 5 6 7 8 9 |
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