export: Export genome browser viewable files
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value Functions Author(s) Examples

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

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)

`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.

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.

NULL

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.

Aaron Taudt

## 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)