genefilter: filtered_p – R documentation

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filtered_p

Compute and adjust p-values, with filtering

Description

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.

Usage

filtered_p(filter, test, theta, data, method = "none")
filtered_R(alpha, filter, test, theta, data, method = "none")

Arguments

`alpha`	A cutoff to which p-values, possibly adjusted for multiple testing, will be compared.
`filter`	A vector of stage-one filter statistics, or a function which is able to compute this vector from `data`, if `data` is supplied.
`test`	A vector of unadjusted p-values, or a function which is able to compute this vector from the filtered portion of `data`, if `data` is supplied. The option to supply a function is useful when the value of the test statistic depends on which hypotheses are filtered out at stage one. (The limma t-statistic is an example.)
`theta`	A vector with one or more filtering fractions to consider. Actual cutoffs are then computed internally by applying `quantile` to the filter statistics contained in (or produced by) the `filter` argument.
`data`	If `filter` and/or `test` are functions rather than vectors of statistics, they will be applied to `data`. The functions will be passed the whole `data` object, and must work over rows, etc. themselves as appropriate.
`method`	The unadjusted p-values contained in (or produced by) `test` will be adjusted for multiple testing after filtering, using the `p.adjust` function in the stats package. See the `method` argument there for options.

Value

For filtered_p, a matrix of p-values, possible adjusted for multiple testing, with one row per null hypothesis and one column per filtering fraction given in theta. For a given column, entries which have been filtered out are NA.

For filtered_R, a count of the entries in the filtered_p result which are less than alpha.

Author(s)

Richard Bourgon <bourgon@ebi.ac.uk>

Examples

# See the vignette: Diagnostic plots for independent filtering

genefilter

genefilter: methods for filtering genes from high-throughput experiments

v1.72.1

Artistic-2.0

Authors

R. Gentleman, V. Carey, W. Huber, F. Hahne

Initial release