Frequency Increment Test

Usage

fit(object, dates, ...)

# S4 method for CountMatrix,missing
fit(object)

# S4 method for CountMatrix,numeric
fit(object, dates)

Arguments

object: A arkhe::CountMatrix object.
dates: A numeric vector of dates.
...: Currently not used.

Value

An IncrementTest object.

Details

The Frequency Increment Test (FIT) rejects neutrality if the distribution of normalized variant frequency increments exhibits a mean that deviates significantly from zero.

References

Feder, A. F., Kryazhimskiy, S. & Plotkin, J. B. (2014). Identifying Signatures of Selection in Genetic Time Series. Genetics, 196(2): 509-522. doi: 10.1534/genetics.113.158220 .

Author

N. Frerebeau

Examples

data("merzbach", package = "folio")

## Coerce the merzbach dataset to a count matrix
## Keep only decoration types that have a maximum frequency of at least 50
keep <- apply(X = merzbach, MARGIN = 2, FUN = function(x) max(x) >= 50)
counts <- as_count(merzbach[, keep])

## Group by phase
## We use the row names as time coordinates (roman numerals)
set_dates(counts) <- as.numeric(utils::as.roman(rownames(counts)))

## Frequency Increment Test
freq <- fit(counts)

## Plot time vs abundance and highlight selection
plot(freq)

plot(freq, roll = TRUE, window = 5)