Export genome browser viewable files

Description

Export multivariate calls and read counts as genome browser viewable file

Usage

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exportMultivariate(hmm, filename, what = c("combinations", "peaks", "counts"),
  exclude.states = "[]", include.states = NULL, trackname = NULL,
  header = TRUE, separate.files = TRUE)

Arguments

hmm

A multiHMM object or file that contains such an object.

filename

The name of the file that will be written. The appropriate ending will be appended, either ".bed.gz" for combinatorial states and peak-calls or ".wig.gz" for read counts. Any existing file will be overwritten.

what

A character vector specifying what will be exported. Supported are c('combinations', 'peaks', 'counts').

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.

trackname

Name that will be used in the "track name" field of the BED file.

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 peaks if what contains 'peaks' or 'counts'.

Details

Export uniHMM objects as files which can be uploaded into a genome browser. Combinatorial states and peak-calls are exported in BED format (.bed.gz) and read counts are exported in WIGGLE format (.wig.gz).

Value

NULL

Author(s)

Aaron Taudt

See Also

exportUnivariates, exportBinnedData

Examples

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## Get an example multiHMM
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
model <- get(load(file))
## Export peak calls and combinatorial states
exportMultivariate(model, filename=tempfile(), what=c('peaks','combinations'))

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