export: Export genome browser viewable files

Description Usage Arguments Details Value Functions Author(s) Examples

Description

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

Usage

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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

Author(s)

Aaron Taudt

Examples

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## 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)

ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.