genefilter: methods for filtering genes from microarray experiments

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Documentation for package ‘genefilter’ version 1.34.0

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allNA A filter function to determine if all elements of a vector are NA.
Anova A filter function for Analysis of Variance
anyNA A filter function to determine if all elements of a vector are NA.
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 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.
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"