exportFiles {chromstaR} | R Documentation

## Export genome browser uploadable files

### Description

These functions allow to export `chromstaR-objects` as files which can be uploaded to a genome browser. Peak calls are exported in BED format (.bed.gz), read counts in wiggle format (.wig.gz) as RPKM values, and combinatorial states are exported in BED format (.bed.gz).

### Usage

    exportPeaks(model, filename, header = TRUE, separate.files = TRUE,
      trackname = NULL)

    exportCounts(model, filename, header = TRUE, separate.files = TRUE,
      trackname = NULL)

    exportCombinations(model, filename, header = TRUE, separate.files = TRUE,
      trackname = NULL, exclude.states = "[]", include.states = NULL)

### Arguments

`model` | A `chromstaR-objects`.
`filename` | The name of the file that will be written. The appropriate ending will be appended, either "_peaks.bed.gz" for peak-calls or "_counts.wig.gz" for read counts or "_combinations.bed.gz" for combinatorial states. Any existing file will be overwritten.
`header` | A logical indicating whether the output file will have a heading track line (`TRUE`) or not (`FALSE`).
`separate.files` | A logical indicating whether or not to produce separate files for each track.
`trackname` | Name that will be used in the "track name" field of the BED file.
`exclude.states` | A character vector with combinatorial states that will be excluded from export.
`include.states` | A character vector with combinatorial states that will be exported. If specified, `exclude.states` is ignored.

### Value

`NULL`

### Functions

- `exportPeaks`: Export peak calls in BED format.

- `exportCounts`: Export read counts as RPKM values in wiggle format.

- `exportCombinations`: Export combinatorial states in BED format.

### Examples

    ## Get an example multiHMM
    file <- system.file("data","combined_mode-differential.RData",
                        package="chromstaR")
    model <- get(load(file))
    ## Export peak calls and combinatorial states
    exportPeaks(model, filename=tempfile())
    exportCombinations(model, filename=tempfile())

[Package chromstaR version 1.13.0 Index]