R/track-2d.R
gtrack.2d.import_contacts.RdCreates a track from a file of inter-genomic contacts.
gtrack.2d.import_contacts(
track = NULL,
description = NULL,
contacts = NULL,
fends = NULL,
allow.duplicates = TRUE
)track name
a character string description
vector of contacts files
name of fragment ends file
if 'TRUE' duplicated contacts are allowed
None.
This function creates a 'Points' (two-dimensional) track from contacts files. If 'allow.duplicates' is 'TRUE' duplicated contacts are allowed and summed up, otherwise an error is reported.
Contacts (coord1, coord2) within the same chromosome are automatically doubled to include also '(coord2, coord1)' unless 'coord1' equals to 'coord2'.
Contacts may come in one or more files.
If 'fends' is 'NULL' contacts file is expected to be in "intervals-value" tab-separated format. The file starts with a header defining the column names. 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. An interval of form (chrom1, start1, end1, chrom2, start2, end2) is added as a point (X, Y) to the resulted track where X = (start1 + end1) / 2 and Y = (start2 + end2) / 2.
One can see an example of "intervals-value" format by running 'gextract' function on a 2D track with a 'file' parameter set to the name of the file.
If 'fends' is not 'NULL' contacts file is expected to be in "fends-value" tab-separated format. It should start with a header containing at least 3 column names 'fend1', 'fend2' and 'count' in arbitrary order followed by lines each defining a contact between two fragment ends.
| COLUMN | VALUE | DESCRIPTION |
| fend1 | Integer | ID of the first fragment end |
| fend2 | Integer | ID of the second fragment end |
| count | Numeric | Value associated with the contact |
A fragment ends file is also in tab-separated format. It should start with a header containing at least 3 column names 'fend', 'chr' and 'coord' in arbitrary order followed by lines each defining a single fragment end.
| COLUMN | VALUE | DESCRIPTION |
| fend | Unique integer | ID of the fragment end |
| chr | Chromosome name | Can be specified with or without "chr" prefix, like: "X" or "chrX" |
| coord | Integer | Coordinate |
'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 contacts 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.