regionFinder {bumphunter} | R Documentation

## Find non-zero regions in vector

### Description

Find regions for which a numeric vector is above (or below) predefined thresholds.

### Usage

    regionFinder(x, chr, pos, cluster = NULL, y = x, summary = mean,
                 ind = seq(along = x), order = TRUE, oneTable = TRUE,
                 maxGap = 300, cutoff=quantile(abs(x), 0.99),
                 assumeSorted = FALSE, verbose = TRUE)

### Arguments

`x` | A numeric vector.
`chr` | A character vector with the chromosomes of each location.
`pos` | A numeric vector representing the genomic location.
`cluster` | The clusters of locations that are to be analyzed together. In the case of microarrays, the cluster is many times supplied by the manufacturer. If not available the function `clusterMaker` can be used.
`y` | A numeric vector with same length as `x` containing values to be averaged for the region summary. See details for more.
`summary` | The function to be used to construct a summary of the `y` values for each region.
`ind` | an optional vector specifying a subset of observations to be used when finding regions.
`order` | if `TRUE` then the resulting tables are ordered based on area of each region. Area is defined as the absolute value of the summarized `y` times the number of features in the regions.
`oneTable` | if `TRUE` only one results table is returned. Otherwise, two tables are returned: one for the regions with positive values and one for the negative values.
`maxGap` | If cluster is not provided this number will be used to define clusters via the `clusterMaker` function.
`cutoff` | This argument is passed to `getSegments`. It represents the upper (and optionally the lower) cutoff for `x`.
`assumeSorted` | This argument is passed to `getSegments` and `clusterMaker`.
`verbose` | Should the function be verbose?

### Details

This function is used in the final steps of `bumphunter`. While `bumphunter` does many things, such as regression and permutation, `regionFinder` simply finds regions that are above a certain threshold (using `getSegments`) and summarizes them. The regions are found based on `x` and the summarized values are based on `y` (which by default equals `x`). The summary is used for the ranking so one might, for example, use t-tests to find regions but summarize using effect sizes.

### Value

If `oneTable` is `FALSE` it returns two tables otherwise it returns one table. The rows of the table are regions. Information on the regions is included in the columns.

### Author(s)

Rafael A Irizarry

### See Also

`bumphunter` for the main usage of this function, `clusterMaker` for the typical input to the `cluster` argument and `getSegments` for a function used within `regionFinder`.

### Examples

    x <- seq(1:1000)
    y <- sin(8*pi*x/1000) + rnorm(1000, 0, 0.2)
    chr <- rep(c(1,2), each=length(x)/2)
    tab <- regionFinder(y, chr, x, cutoff=0.8)
    print(tab[tab$L>10,])

[Package bumphunter version 1.22.0 Index]