misha (version 5.4.0)

gcor: 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
)

Value

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

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.

See Also

gextract, gscreen, gsummary

Examples

# \dontshow{
old <- options(gmax.processes = 2, gmultitasking = FALSE, gmax.data.size = 1e5)
# }

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"
)

# \dontshow{
options(old)
# }