gtrack.import_set: Creates one or more tracks from multiple WIG / BigWig /...

In misha: Toolkit for Analysis of Genomic Data

Creates one or more tracks from multiple WIG / BigWig / BedGraph / tab-delimited files on disk or FTP

Description

Creates one or more tracks from WIG / BigWig / BedGraph / tab-delimited files on disk or FTP.

Usage

gtrack.import_set(
  description = NULL,
  path = NULL,
  binsize = NULL,
  track.prefix = NULL,
  defval = NaN
)

Arguments

description	a character string description
path	file path or URL (may contain wildcards)
binsize	bin size of the newly created 'Dense' track or '0' for a 'Sparse' track
track.prefix	prefix for a track name
defval	default track value

Details

This function is similar to 'gtrack.import' however unlike the latter it can create multiple tracks. Additionally the files can be fetched from an FTP server.

The files are expected to be in WIG / BigWig / BedGraph / tab-delimited formats. One can learn about the format of the tab-delimited file by running 'gextract' function with a 'file' parameter set to the name of the file. Zipped files are supported (file name must have '.gz' or '.zip' suffix).

Files are specified by 'path' argument. 'path' can be also a URL of an FTP server in the form of 'ftp://[address]/[files]'. If 'path' is a URL, the files are first downloaded from FTP server to a temporary directory and then imported to tracks. The temporary directory is created at 'GROOT/downloads'.

Regardless whether 'path' is file path or to a URL, it can contain wildcards. Hence multiple files can be imported (and downloaded) at once.

If 'binsize' is 0 the resulted tracks are created in 'Sparse' format. Otherwise the 'Dense' format is chosen with a bin size equal to 'binsize'. The values that were not defined in input file file are substituted by 'defval' value.

The name of a each created track is of '[track.prefix][filename]' form, where 'filename' is the name of the WIG file. For example, if 'track.prefix' equals to "wigs."" and an input file name is 'mydata', a track named 'wigs.mydata' is created. If 'track.prefix' is 'NULL' no prefix is appended to the name of the created track.

Existing tracks are not overwritten and no new directories are automatically created.

'description' is added to the created tracks as an attribute.

'gtrack.import_set' does not stop if an error occurs while importing a file. It rather continues importing the rest of the files.

'gtrack.import_set' returns the names of the files that were successfully imported and those that failed.

Value

Names of files that were successfully imported and those that failed.

See Also

gtrack.import, gwget, gtrack.rm, gtrack.info, gdir.create, gextract

misha documentation built on Sept. 14, 2023, 5:08 p.m.