Creates an array track from array tracks or files.
gtrack.array.import(track = NULL, description = NULL, ...)None.
This function creates a new 'Array' track from one or more "sources". Each source can be either another 'Array' track or a tab-delimited file that contains one-dimensional intervals and column values that should be added to the newly created track. One can learn about the exact format of the file by running 'gtrack.array.extract' or 'gextract' functions with a 'file' parameter and inspecting the output file.
There might be more than one source used to create the new track. In that case the new track will contain the columns from all the sources. The equally named columns are merged. Intervals that appear in one source but not in the other are added and the values for the missing columns are set to NaN. Intervals with all NaN values are not added. Partial overlaps between two intervals from different sources are forbidden.
'description' is added as a track attribute.
f1 <- tempfile()
gextract("sparse_track", gintervals(1, 5000, 20000), file = f1)
f2 <- tempfile()
gtrack.array.extract("array_track", c("col2", "col3", "col4"),
gintervals(1, 0, 20000),
file = f2
)
f3 <- tempfile()
gtrack.array.extract("array_track", c("col1", "col3"),
gintervals(1, 0, 20000),
file = f3
)
gtrack.array.import("test_track1", "Test array track 1", f1, f2)
gtrack.array.extract("test_track1", NULL, .misha$ALLGENOME)
#> chrom start end sparse_track col2 col3 col4 intervalID
#> 1 chr1 0 50 NaN 2 NaN 4 1
#> 2 chr1 100 150 NaN 102 NaN NaN 1
#> 3 chr1 250 300 NaN NaN 203 NaN 1
#> 4 chr1 1400 1450 NaN 302 303 304 1
#> 5 chr1 4750 4800 NaN 402 NaN 404 1
#> 6 chr1 6350 6400 0.44 502 NaN NaN 1
#> 7 chr1 9900 9950 0.36 NaN 603 604 1
#> 8 chr1 10400 10450 0.44 702 NaN NaN 1
#> 9 chr1 10550 10600 0.36 NaN 803 804 1
#> 10 chr1 12150 12200 0.40 NaN 903 NaN 1
#> 11 chr1 12650 12700 0.40 1002 1003 1004 1
#> 12 chr1 13550 13600 0.36 1102 1103 NaN 1
#> 13 chr1 14300 14350 0.36 1202 1203 1204 1
#> 14 chr1 15100 15150 0.40 1302 1303 1304 1
#> 15 chr1 15200 15250 0.40 1402 1403 1404 1
#> 16 chr1 16500 16550 0.36 NaN 1503 NaN 1
#> 17 chr1 16750 16800 0.40 1602 NaN 1604 1
#> 18 chr1 16950 17000 0.48 1702 NaN 1704 1
#> 19 chr1 17050 17100 0.44 1802 1803 1804 1
#> 20 chr1 17250 17300 0.56 1902 1903 1904 1
#> 21 chr1 17750 17800 0.48 NaN 2003 2004 1
#> 22 chr1 18000 18050 0.36 2102 2103 2104 1
#> 23 chr1 18250 18300 0.48 NaN 2203 2204 1
gtrack.array.import(
"test_track2", "Test array track 2",
"test_track1", f3
)
gtrack.array.extract("test_track2", NULL, .misha$ALLGENOME)
#> chrom start end sparse_track col2 col3 col4 col1 intervalID
#> 1 chr1 0 50 NaN 2 NaN 4 NaN 1
#> 2 chr1 100 150 NaN 102 NaN NaN NaN 1
#> 3 chr1 250 300 NaN NaN 203 NaN 201 1
#> 4 chr1 1400 1450 NaN 302 303 304 301 1
#> 5 chr1 4750 4800 NaN 402 NaN 404 401 1
#> 6 chr1 6350 6400 0.44 502 NaN NaN 501 1
#> 7 chr1 9900 9950 0.36 NaN 603 604 NaN 1
#> 8 chr1 10400 10450 0.44 702 NaN NaN 701 1
#> 9 chr1 10550 10600 0.36 NaN 803 804 NaN 1
#> 10 chr1 12150 12200 0.40 NaN 903 NaN 901 1
#> 11 chr1 12650 12700 0.40 1002 1003 1004 1001 1
#> 12 chr1 13550 13600 0.36 1102 1103 NaN 1101 1
#> 13 chr1 14300 14350 0.36 1202 1203 1204 1201 1
#> 14 chr1 15100 15150 0.40 1302 1303 1304 1301 1
#> 15 chr1 15200 15250 0.40 1402 1403 1404 1401 1
#> 16 chr1 16500 16550 0.36 NaN 1503 NaN NaN 1
#> 17 chr1 16750 16800 0.40 1602 NaN 1604 NaN 1
#> 18 chr1 16950 17000 0.48 1702 NaN 1704 NaN 1
#> 19 chr1 17050 17100 0.44 1802 1803 1804 NaN 1
#> 20 chr1 17250 17300 0.56 1902 1903 1904 1901 1
#> 21 chr1 17750 17800 0.48 NaN 2003 2004 NaN 1
#> 22 chr1 18000 18050 0.36 2102 2103 2104 2101 1
#> 23 chr1 18250 18300 0.48 NaN 2203 2204 NaN 1
gtrack.rm("test_track1", TRUE)
gtrack.rm("test_track2", TRUE)
unlink(c(f1, f2, f3))