gintervals.update: Updates a named intervals set

In misha: Toolkit for Analysis of Genomic Data

Updates a named intervals set

Description

Updates a named intervals set.

Usage

gintervals.update(
  intervals.set = NULL,
  intervals = "",
  chrom = NULL,
  chrom1 = NULL,
  chrom2 = NULL
)

Arguments

intervals.set	name of an intervals set
intervals	intervals or 'NULL'
chrom	chromosome for 1D intervals set
chrom1	first chromosome for 2D intervals set
chrom2	second chromosome for 2D intervals set

Details

This function replaces all intervals of given chromosome (or chromosome pair) within 'intervals.set' with 'intervals'. Chromosome is specified by 'chrom' for 1D intervals set or 'chrom1', 'chrom2' for 2D intervals set.

If 'intervals' is 'NULL' all intervals of given chromosome are removed from 'intervals.set'.

Value

None.

See Also

gintervals.save, gintervals.load, gintervals.exists, gintervals.ls

Examples

gdb.init_examples()
intervs <- gscreen(
    "sparse_track > 0.2",
    gintervals(c(1, 2), 0, 10000)
)
gintervals.save("testintervs", intervs)
gintervals.load("testintervs")
gintervals.update("testintervs", intervs[intervs$chrom == "chr2", ][1:5, ], chrom = 2)
gintervals.load("testintervs")
gintervals.update("testintervs", NULL, chrom = 2)
gintervals.load("testintervs")
gintervals.rm("testintervs", force = TRUE)

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