Use fread() function with cmd argument with a shell command that pre-processes the file(s).
Example: use grep first and only have fread() process output of that command:
library(data.table)
dataDir <- path.expand("~/dataexpo")
dataFiles <- dir(dataDir, pattern = "csv$", full.names = TRUE)
# All flights by American Airlines
command <- sprintf("grep --text ',AA,' %s", paste(dataFiles, collapse = " "))
dt <- data.table::fread(cmd = command)