# genefilter: methods for filtering genes from high-throughput experiments

## Documentation for package ‘genefilter’ version 1.60.0

- 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.
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"