Passing grouping variables to bed_map

[jayhesselberth]

Need a way to pass grouping variables to bed_map, e.g., window intervals from makewindows:

tss_intervals %>%
  bed_flank(size = 1000) %>%
  bed_makewindows(win_size = 50, win_id = 'num') %>%
  bed_map(chip_signal, groups = .win_id, sum = sum(value))

bed_map <- function(..., groups, ...) {
  res <- bed_intersect(bed_tbl, signal_tbl, suffix_y = '') %>%
    group_by_(groups) %>%
    summarize_(.dots = lazyeval::lazy_dots(...)) %>%
    rename(start = start.x, end = end.x)
}

Need more flexible way to specific default grouping by chrom, start.x, end.x. Maybe have a unique ID for each intersection and group_by that?

[jayhesselberth]

This is one approach, need to propagate groupings in bed_map:

bed_makewindows(win_size = 50, win_id = 'num') %>%
group_by(win_id) %>%
bed_map(chip_signal, sum = sum(value))

Alternatively

bed_makewindows(win_size = 50, win_id = 'num') %>%
bed_map(chip_signal, map_value = sum(value)) %>%
group_by(win_id) %>%
summarize(signal_mean = mean(map_value), signal_var = var(map_value)

I favor the second one as it's closer to the original. But this is currently broken as win_id will have a .y suffix from bed_intersect. This seems to be a recurring problem. One solution would be to only suffix the start and end colnames in bed_intersect.

[jayhesselberth]

closed by e809ea2