Filter sparse time points and lineages

Removes time points with very low total counts and lineages observed at too few time points.

Usage

filter_sparse(x, min_total = 10L, min_timepoints = 3L)

Arguments

x

An lfq_data object.

min_total

Minimum total sequences per time point. Default 10.

min_timepoints

Minimum number of time points a lineage must appear to be retained. Default 3.

Value

An lfq_data object with sparse entries removed.

Examples

sim <- simulate_dynamics(n_lineages = 3,
  advantages = c("A" = 1.2, "B" = 0.8), seed = 1)
filtered <- filter_sparse(sim, min_total = 100)