genefilter: methods for filtering genes from high-throughput experiments

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Documentation for package ‘genefilter’ version 1.86.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Anova	A filter function for Analysis of Variance
area	Class "rowROC"
area-method	Class "rowROC"
AUC	Class "rowROC"
AUC-method	Class "rowROC"
colFtests	t-tests and F-tests for rows or columns of a matrix
colFtests-method	t-tests and F-tests for rows or columns of a matrix
colttests	t-tests and F-tests for rows or columns of a matrix
colttests-method	t-tests and F-tests for rows or columns of a matrix
coxfilter	A filter function for univariate Cox regression.
cv	A filter function for the coefficient of variation.
dist2	Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix.
eSetFilter	A function to filter an eSet object
fastT	t-tests and F-tests for rows or columns of a matrix
featureFilter	Filtering of Features in an ExpressionSet
filtered_p	Compute and adjust p-values, with filtering
filtered_R	Compute and adjust p-values, with filtering
filterfun	Creates a first FALSE exiting function from the list of filter functions it is given.
filter_volcano	Volcano plot for overall variance filtering
findLargest	Find the Entrez Gene ID corresponding to the largest statistic
gapFilter	A filter to select genes based on there being a gap.
genefilter	A function to filter genes.
genefilter-deprecated	Deprecated functions in package 'genefilter'
genefinder	Finds genes that have similar patterns of expression.
genefinder-method	Finds genes that have similar patterns of expression.
genescale	Scales a matrix or vector.
getFilterNames	A function to filter an eSet object
getFuncDesc	A function to filter an eSet object
getRdAsText	A function to filter an eSet object
half.range.mode	Mode estimation for continuous data
isESet	A function to filter an eSet object
kappa_p	Compute proportionality constant for fold change bound.
kappa_t	Compute proportionality constant for fold change bound.
kOverA	A filter function for k elements larger than A.
maxA	A filter function to filter according to the maximum.
nsFilter	Filtering of Features in an ExpressionSet
nsFilter-method	Filtering of Features in an ExpressionSet
parseArgs	A function to filter an eSet object
parseDesc	A function to filter an eSet object
pAUC	Class "rowROC"
pAUC-method	Class "rowROC"
plot-method	Class "rowROC"
pOverA	A filter function to filter according to the proportion of elements larger than A.
rejection_plot	Plot rejections vs. p-value cutoff
rowFtests	t-tests and F-tests for rows or columns of a matrix
rowFtests-method	t-tests and F-tests for rows or columns of a matrix
rowpAUCs	Rowwise ROC and pAUC computation
rowpAUCs-method	Rowwise ROC and pAUC computation
rowpAUCs-methods	Rowwise ROC and pAUC computation
rowROC	Class "rowROC"
rowROC-class	Class "rowROC"
rowSds	Row variance and standard deviation of a numeric array
rowttests	t-tests and F-tests for rows or columns of a matrix
rowttests-method	t-tests and F-tests for rows or columns of a matrix
rowVars	Row variance and standard deviation of a numeric array
sens	Class "rowROC"
sens-method	Class "rowROC"
setESetArgs	A function to filter an eSet object
shorth	A location estimator based on the shorth
show-method	Class "rowROC"
showESet	A function to filter an eSet object
spec	Class "rowROC"
spec-method	Class "rowROC"
tdata	A small test dataset of Affymetrix Expression data.
ttest	A filter function for a t.test
varFilter	Filtering of Features in an ExpressionSet
[-method	Class "rowROC"