gtrack.2d.import: Creates a 2D track from tab-delimited file

In misha: Toolkit for Analysis of Genomic Data

Creates a 2D track from tab-delimited file

Description

Creates a 2D track from tab-delimited file(s).

Usage

gtrack.2d.import(track = NULL, description = NULL, file = NULL)

Arguments

track	track name
description	a character string description
file	vector of file paths

Details

This function creates a 2D track track from one or more tab-delimited files. Each file must start with a header describing the columns. The first 6 columns must have the following names: 'chrom1', 'start1', 'end1', 'chrom2', 'start2', 'end2'. The last column is designated for the value and it may have an arbitrary name. The header is followed by a list of intervals and a value for each interval. Overlapping intervals are forbidden.

One can learn about the format of the tab-delimited file by running 'gextract' function on a 2D track with a 'file' parameter set to the name of the file.

If all the imported intervals represent a point (i.e. end == start + 1) a 'Points' track is created otherwise it is a 'Rectangles' track.

'description' is added as a track attribute.

Note: temporary files are created in the directory of the track during the run of the function. A few of them need to be kept simultaneously open. If the number of chromosomes and / or intervals is particularly high, a few thousands files might be needed to be opened simultaneously. Some operating systems limit the number of open files per user, in which case the function might fail with "Too many open files" or similar error. The workaround could be:

1. Increase the limit of simultaneously opened files (the way varies depending on your operating system). 2. Increase the value of 'gmax.data.size' option. Higher values of 'gmax.data.size' option will increased memory usage of the function but create fewer temporary files.

Value

None.

See Also

gtrack.rm, gtrack.info, gdir.create

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