exportFiles: Export genome browser uploadable files

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

These functions allow to export chromstaR-objects as files which can be uploaded to a genome browser. Peak calls are exported in BED format (.bed.gz), read counts in wiggle format (.wig.gz) as RPKM values, and combinatorial states are exported in BED format (.bed.gz).

Usage

exportPeaks(
  model,
  filename,
  header = TRUE,
  separate.files = TRUE,
  trackname = NULL
)

exportCounts(
  model,
  filename,
  header = TRUE,
  separate.files = TRUE,
  trackname = NULL
)

exportCombinations(
  model,
  filename,
  header = TRUE,
  separate.files = TRUE,
  trackname = NULL,
  exclude.states = "[]",
  include.states = NULL
)

Arguments

model	A chromstaR-objects.
filename	The name of the file that will be written. The appropriate ending will be appended, either "_peaks.bed.gz" for peak-calls or "_counts.wig.gz" for read counts or "_combinations.bed.gz" for combinatorial states. Any existing file will be overwritten.
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 each track.
trackname	Name that will be used in the "track name" field of the BED file.
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.

Value

NULL

Functions

• exportPeaks: Export peak calls in BED format.

• exportCounts: Export read counts as RPKM values in wiggle format.

• exportCombinations: Export combinatorial states in BED format.

Examples

## Get an example multiHMM
file <- system.file("data","combined_mode-differential.RData",
                    package="chromstaR")
model <- get(load(file))
## Export peak calls and combinatorial states
exportPeaks(model, filename=tempfile())
exportCombinations(model, filename=tempfile())

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.