export: Export genome browser viewable files

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

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)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.