Removes lowly expressed genes

Usage

ts_filter(data, min_reads = 5, min_prop = 3/5)

Arguments

data

A tibble or data.frame containing columns:

target_id (character): Transcript identifiers
time (numeric): Time point of measurement
counts (numeric): Read counts

min_reads

minimum reads per transcript per sample

min_prop

minimum proportion of samples that exceed min_read at a given time point (default: 3/5)

Value

a character vector of transcript IDs to keep

Details

Identifies targets that show strong and consistent expression in at least one timepoint. For each timepoint, the function calculates the proportion of samples where a targets exceeds min_reads. Targets are retained if they meet the minimum proportion (min_prop) at any timepoint in the experiment.

Examples

data <- dplyr::tibble(
  target_id = rep(paste0("t", 1:3), each = 6),
  time = rep(c(0, 4, 8), 6),
  counts = c(6,6,6, 0,0,0, 6,0,6, 0,6,6, 6,6,6, 6,0,0)
)
ts_filter(data)
#> [1] "t2" "t3"