Anova
(Package: genefilter) :
A filter function for Analysis of Variance
Anova returns a function of one argument with bindings for cov and p. The function, when evaluated, performs an ANOVA using cov as the covariate. It returns TRUE if the p value for a difference in means is less than p.
● Data Source:
BioConductor
● Keywords: manip
● Alias: Anova
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coxfilter
(Package: genefilter) :
A filter function for univariate Cox regression.
A function that performs Cox regression with bindings for surt, cens, and p is returned. This function filters genes according to the attained p-value from a Cox regression using surt as the survival times, and cens as the censoring indicator. It requires survival.
● Data Source:
BioConductor
● Keywords: manip
● Alias: coxfilter
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cv
(Package: genefilter) :
A filter function for the coefficient of variation.
cv returns a function with values for a and b bound. This function takes a single argument. It computes the coefficient of variation for the input vector and returns TRUE if the coefficient of variation is between a and b. Otherwise it returns FALSE
● Data Source:
BioConductor
● Keywords: manip
● Alias: cv
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Calculate an n-by-n matrix by applying a function to all pairs of columns of an m-by-n matrix.
● Data Source:
BioConductor
● Keywords: manip
● Alias: dist2
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eSetFilter
(Package: genefilter) :
A function to filter an eSet object
Given a Bioconductor's ExpressionSet object, this function filters genes using a set of selected filters.
● Data Source:
BioConductor
● Keywords: manip
● Alias: eSetFilter, getFilterNames, getFuncDesc, getRdAsText, isESet, parseArgs, parseDesc, setESetArgs, showESet
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filter_volcano
(Package: genefilter) :
Volcano plot for overall variance filtering
Generate a volcano plot contrasting p-value with fold change (on the log scale), in order to visualize the effect of filtering on overall variance and also assign significance via p-value.
● Data Source:
BioConductor
● Keywords:
● Alias: filter_volcano
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Given filter and test statistics in the form of unadjusted p-values, or functions able to compute these statistics from the data, filter and then correct the p-values across a range of filtering stringencies.
● Data Source:
BioConductor
● Keywords:
● Alias: filtered_R, filtered_p
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filterfun
(Package: genefilter) :
Creates a first FALSE exiting function from the list of
This function creates a function that takes a single argument. The filtering functions are bound in the environment of the returned function and are applied sequentially to the argument of the returned function. When the first filter function evaluates to FALSE the function returns FALSE otherwise it returns TRUE.
● Data Source:
BioConductor
● Keywords: manip
● Alias: filterfun
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findLargest
(Package: genefilter) :
Find the Entrez Gene ID corresponding to the largest statistic
Most microarrays have multiple probes per gene (Entrez). This function finds all replicates, and then selects the one with the largest value of the test statistic.
● Data Source:
BioConductor
● Keywords: manip
● Alias: findLargest
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gapFilter
(Package: genefilter) :
A filter to select genes based on there being a gap.
The gapFilter looks for genes that might usefully discriminate between two groups (possibly unknown at the time of filtering). To do this we look for a gap in the ordered expression values. The gap must come in the central portion (we exclude jumps in the initial Prop values or the final Prop values). Alternatively, if the IQR for the gene is large that will also pass our test and the gene will be selected.
● Data Source:
BioConductor
● Keywords: manip
● Alias: gapFilter
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