R/update_filter.R

In ndbrown6/MSK-GRAIL-TECHVAL: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

'update_filter' <- function(filter,
			    qualnobaq,
			    pgtkxgdna,
			    is_edge,
			    min_p,
			    min_qual = 60,
			    sep = ";")
{
	high_qual = which(qualnobaq >= min_qual)
	low_qual = which(qualnobaq < min_qual)
	gdna = which(pgtkxgdna < min_p)
	edge = which(is_edge)
	pass = high_qual %>%
	       setdiff(gdna) %>%
	       setdiff(edge)
	low_qual_string = sprintf("QUAL_LT_%d", min_qual)
	gdna_strings = sprintf("PGTKXGDNA_LT_%0.2f", min_p)
	edge_string = "IS_EDGE"
  
	ids = data_frame(i = seq_along(filter))
	filters = bind_rows(
			data_frame(i = pass, filter = "PASS"),
			data_frame(i = low_qual, filter = low_qual_string),
			data_frame(i = gdna, filter = gdna_strings[gdna]),
			data_frame(i = edge, filter = edge_string))
	filters = filters %>%
		  group_by(i) %>%
		  summarize(filter = str_c(filter, collapse = sep)) %>%
		  ungroup() %>%
		  full_join(ids) %>%
		  arrange(i)
	return(invisible(filters$filter[filters$i]))
}