makeWindows {EnrichedHeatmap} | R Documentation

## Split Regions into Windows

### Description

Split Regions into Windows

### Usage

    makeWindows(query, w = NULL, k = NULL, direction = c("normal", "reverse"),
        short.keep = FALSE)

### Arguments

`query` | A `GRanges-class` object.
`w` | Window size. A value larger than 1 means the number of base pairs and a value between 0 and 1 is the percent to the current region.
`k` | Number of partitions for each region. If it is set, all other arguments are ignored.
`direction` | Where to start the splitting? See 'Details' section.
`short.keep` | If the the region can not be split equally under the window size, the argument controls whether to keep the windows that are smaller than the window size. See 'Details' section.

### Details

Following illustrates the meaning of `direction` and `short.keep`:

        -->-->-->-  one region, split by 3bp window (">" represents the direction of the sequence)
        aaabbbccc   direction = "normal",  short.keep = FALSE
        aaabbbcccd  direction = "normal",  short.keep = TRUE
         aaabbbccc  direction = "reverse", short.keep = FALSE
        abbbcccddd  direction = "reverse", short.keep = TRUE

### Value

A `GRanges-class` object with two additional columns attached:

- `.i_query` which contains the correspondance between small windows and original regions in `query`

- `.i_window` which contains the index of the small window on the current region.

### Author(s)

Zuguang gu <z.gu@dkfz.de>

### Examples

    query = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 21), end = c(10, 20, 30)))
    makeWindows(query, w = 2)
    makeWindows(query, w = 0.5)
    makeWindows(query, w = 3)
    makeWindows(query, w = 3, direction = "reverse")
    makeWindows(query, w = 3, short.keep = TRUE)
    makeWindows(query, w = 3, direction = "reverse", short.keep = TRUE)
    makeWindows(query, w = 12)
    makeWindows(query, w = 12, short.keep = TRUE)
    makeWindows(query, k = 2)
    makeWindows(query, k = 3)
    query = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 31), end = c(10, 30, 70)))
    makeWindows(query, w = 2)
    makeWindows(query, w = 0.2)

[Package EnrichedHeatmap version 1.16.0 Index]