gcor: Calculates correlation between track expressions

In misha: Toolkit for Analysis of Genomic Data

Calculates correlation between track expressions

Description

Calculates correlation between track expressions over iterator bins inside the supplied genomic scope. Expressions are processed in pairs: (expr1, expr2), (expr3, expr4), etc. Only bins where both expressions are not NaN are used.

Usage

gcor(
  expr1 = NULL,
  expr2 = NULL,
  ...,
  intervals = NULL,
  iterator = NULL,
  band = NULL,
  method = c("pearson", "spearman", "spearman.exact"),
  details = FALSE,
  names = NULL
)

Arguments

expr1	first track expression
expr2	second track expression
...	additional track expressions, supplied as pairs (expr3, expr4, ...)
intervals	genomic scope for which the function is applied
iterator	track expression iterator. If 'NULL' iterator is determined implicitly based on track expression.
band	track expression band. If 'NULL' no band is used.
method	correlation method to use. One of 'pearson' (default), 'spearman' (approximate, memory-efficient), or 'spearman.exact' (exact, requires O(n) memory where n is number of non-NaN pairs).
details	if 'TRUE' returns summary statistics for each pair, otherwise returns correlations only. For Pearson, includes n, n.na, mean1, mean2, sd1, sd2, cov, cor. For Spearman methods, includes n, n.na, cor.
names	optional names for the pairs. If supplied, length must match the number of pairs.

Value

If 'details' is 'FALSE', a numeric vector of correlations. If 'details' is 'TRUE', a data frame with summary statistics for each pair.

See Also

gextract, gscreen, gsummary

Examples

gdb.init_examples()
gcor("dense_track", "sparse_track", intervals = gintervals(1, 0, 10000), iterator = 1000)

# Spearman correlation (approximate, memory-efficient)
gcor("dense_track", "sparse_track",
    intervals = gintervals(1, 0, 10000),
    iterator = 1000, method = "spearman"
)

# Exact Spearman correlation
gcor("dense_track", "sparse_track",
    intervals = gintervals(1, 0, 10000),
    iterator = 1000, method = "spearman.exact"
)

misha documentation built on Jan. 28, 2026, 1:07 a.m.