export {AneuFinder} | R Documentation

## Export genome browser viewable files

### Description

Export copy-number-variation state or read counts as genome browser viewable file

### Usage

    exportCNVs(hmms, filename, trackname = NULL, cluster = TRUE,
      export.CNV = TRUE, export.breakpoints = TRUE)

    exportReadCounts(hmms, filename)

    exportGRanges(gr, filename, header = TRUE, trackname = NULL, score = NULL,
      priority = NULL, append = FALSE, chromosome.format = "UCSC",
      thickStart = NULL, thickEnd = NULL, as.wiggle = FALSE, wiggle.val)

### Arguments

`hmms` | A list of `aneuHMM` objects or a character vector with files that contain such objects.
`filename` | The name of the file that will be written. The appropriate ending will be appended, either ".bed.gz" for CNV-state or ".wig.gz" for read counts. Any existing file will be overwritten.
`trackname` | The name that will be used as track name and description in the header.
`cluster` | If `TRUE`, the samples will be clustered by similarity in their CNV-state.
`export.CNV` | A logical, indicating whether the CNV-state shall be exported.
`export.breakpoints` | A logical, indicating whether breakpoints shall be exported.
`gr` | A `GRanges-class` object.
`header` | A logical indicating whether the output file will have a heading track line (`TRUE`) or not (`FALSE`).
`score` | A vector of the same length as `gr`, which will be used for the 'score' column in the BED file.
`priority` | Priority of the track for display in the genome browser.
`append` | Append to `filename`.
`chromosome.format` | A character specifying the format of the chromosomes if `assembly` is specified. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...).#' @importFrom utils write.table
`thickStart, thickEnd` | A vector of the same length as `gr`, which will be used for the 'thickStart' and 'thickEnd' columns in the BED file.
`as.wiggle` | A logical indicating whether a variableStep-wiggle file will be exported instead of a BED file. If `TRUE`, `wiggle.value` must be specified.
`wiggle.val` | A vector of the same length as `gr`, which will be used for the values in the wiggle file.

### Details

Use `exportCNVs` to export the copy-number-variation state from an `aneuHMM` object in BED format. Use `exportReadCounts` to export the binned read counts from an `aneuHMM` object in WIGGLE format. Use `exportGRanges` to export a `GRanges-class` object in BED format.

### Value

`NULL`

### Functions

- `exportCNVs`: Export CNV-state as .bed.gz file

- `exportReadCounts`: Export binned read counts as .wig.gz file

- `exportGRanges`: Export `GRanges-class` object as BED file.

### Author(s)

Aaron Taudt

### Examples

    ## Not run:
    ## Get results from a small-cell-lung-cancer
    folder <- system.file("extdata", "primary-lung", "hmms", package="AneuFinderData")
    files <- list.files(folder, full.names=TRUE)
    ## Export the CNV states for upload to the UCSC genome browser
    exportCNVs(files, filename='upload-me-to-a-genome-browser', cluster=TRUE)
    ## End(Not run)

[Package AneuFinder version 1.20.0 Index]