data-raw/hotspots.R

In kpjonsson/annotate-maf: Functional Annotation of Variants in a MAF File

# Generate hotspot list -------------------------------------------------------------------------------------------
hs_from_local = c('/luna/work/hotspots/data/nbt-cd24k-FP-filtered-hotspots.txt',
                  '/luna/work/hotspots/3d/hotspots.txt')

hs_from_cluster = c('/ifs/work/taylorlab/jonssonp/hotspots/data/nbt-cd24k-FP-filtered-hotspots.txt',
                    '/ifs/work/taylorlab/jonssonp/hotspots/3d/hotspots.txt')

if (Sys.info()[['nodename']] == 'lski2423') {
    hotspot_files =  hs_from_local
} else {
    hotspot_files = hs_from_cluster
}

hotspots = map_dfr(hotspot_files, function(x) {
    fread(x) %>%
        mutate(source = x,
               Type = if('Type' %in% names(.)) { Type } else { 'single residue' },
               Class = if('Class' %in% names(.)) { Class } else { 'single residue' },
               false_positive = if('false_positive' %in% names(.)) { false_positive } else { FALSE },
               previous_mutations = if('previous_mutations' %in% names(.)) { previous_mutations } else { str_replace_all(Variants, ':[0-9]+\\|?', ',') })
}) %>%
    mutate(indel_hotspot = Type == 'in-frame indel',
           indel_hotspot = ifelse(is.na(indel_hotspot), FALSE, indel_hotspot),
           threeD_hotspot = ifelse(Class %in% c('Hotspot-linked', 'Cluster-exclusive'), TRUE, FALSE),
           snv_hotspot = source %like% 'NBT|24k' & indel_hotspot == FALSE,
           Pos = ifelse(indel_hotspot == F, str_extract(Residue, '(?<=[A-Z])[0-9]+'), NA),
           Start = ifelse(indel_hotspot == T, str_extract(Residue, '^[0-9]+(?=-)'), NA),
           End = ifelse(indel_hotspot == T, str_extract(Residue, '(?<=-)[0-9]+$'), NA),
           Pos = ifelse(indel_hotspot == T & is.na(Start), Residue, Pos)) %>%
    replace_na(list(false_positive = FALSE)) %>%
    group_by(Gene, Residue, Pos, Start, End) %>%
    dplyr::summarize(indel_hotspot = any(indel_hotspot == T, na.rm = T),
                     snv_hotspot = any(snv_hotspot == T, na.rm = T),
                     threeD_hotspot = any(threeD_hotspot == T, na.rm = T),
                     previous_mutations = paste(c(unique(unlist(strsplit(previous_mutations, ',')))), collapse = ','),
                     false_positive = all(false_positive == T, na.rm = T)) %>%
    ungroup() %>%
    mutate(tag = str_c(Gene, Pos),
           Pos = as.numeric(Pos),
           Start = as.numeric(Start),
           End = as.numeric(End)) %>%
    filter(false_positive == FALSE) %>%
    select(-false_positive)

usethis::use_data(hotspots)