gintervals.neighbors: Finds neighbors between two sets of intervals

In misha: Toolkit for Analysis of Genomic Data

Finds neighbors between two sets of intervals

Description

Finds neighbors between two sets of intervals.

Usage

gintervals.neighbors(
  intervals1 = NULL,
  intervals2 = NULL,
  maxneighbors = 1,
  mindist = -1e+09,
  maxdist = 1e+09,
  mindist1 = -1e+09,
  maxdist1 = 1e+09,
  mindist2 = -1e+09,
  maxdist2 = 1e+09,
  na.if.notfound = FALSE,
  intervals.set.out = NULL
)

Arguments

intervals1, intervals2	intervals
maxneighbors	maximal number of neighbors
mindist, maxdist	distance range for 1D intervals
mindist1, maxdist1, mindist2, maxdist2	distance range for 2D intervals
na.if.notfound	if 'TRUE' return 'NA' interval if no matching neighbors were found, otherwise omit the interval in the answer
intervals.set.out	intervals set name where the function result is optionally outputted

Details

This function finds for each interval in 'intervals1' the closest 'maxneighbors' intervals from 'intervals2'.

For 1D intervals the distance must fall in the range of ['mindist', 'maxdist']. If 'intervals2' contains a 'strand' column the distance can be positive or negative depending on the 'strand' value and the position of interval2 relatively to interval1. If 'strand' column is missing the distance is always positive.

For 2D intervals two distances are calculated and returned for each axis. The distances must fall in the range of ['mindist1', 'maxdist1'] for axis 1 and ['mindist2', 'maxdist2'] for axis 2. For selecting the closest 'maxneighbors' intervals Manhattan distance is used (i.e. dist1+dist2).

The names of the returned columns are made unique using make.unique(colnames(df), sep = ""), assuming 'df' is the result.

If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.

Value

If 'intervals.set.out' is 'NULL' a data frame containing the pairs of intervals from 'intervals1', intervals from 'intervals2' and an additional column named 'dist' ('dist1' and 'dist2' for 2D intervals) representing the distance between the corresponding intervals. The intervals from intervals2 would be changed to 'chrom1', 'start1', and 'end1' and for 2D intervals chrom11, start11, end11 and chrom22, start22, end22. If 'na.if.notfound' is 'TRUE', the data frame contains all the intervals from 'intervals1' including those for which no matching neighbor was found. For the latter intervals an 'NA' neighboring interval is stated. If 'na.if.notfound' is 'FALSE', the data frame contains only intervals from 'intervals1' for which matching neighbor(s) was found.

See Also

gintervals,

Examples

gdb.init_examples()
intervs1 <- giterator.intervals("dense_track",
    gintervals(1, 0, 4000),
    iterator = 233
)
intervs2 <- giterator.intervals(
    "sparse_track",
    gintervals(1, 0, 2000)
)
gintervals.neighbors(intervs1, intervs2, 10,
    mindist = -300,
    maxdist = 500
)
intervs2$strand <- c(1, 1, -1, 1)
gintervals.neighbors(intervs1, intervs2, 10,
    mindist = -300,
    maxdist = 500
)

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