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sort regions by mutation coverage #24

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sort regions by mutation coverage #24

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17 changes: 11 additions & 6 deletions R/eval_region.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,7 @@ eval_regions <- function(reg_to_patient_mut){
# basic region annotation
unique_reg <- reg_to_patient_mut %>%
filter(!is.na(reg_id)) %>%
distinct(reg_id, reg_chr, reg_start, reg_end) %>%
mutate(
n_region = row_number(),
reg_size = reg_end - reg_start + 1,
reg_size_cum = cumsum(reg_size)
)
distinct(reg_id, reg_chr, reg_start, reg_end)

# total number of patients for each region
reg_to_n_patient <- reg_to_patient_mut %>%
Expand All @@ -42,6 +37,16 @@ eval_regions <- function(reg_to_patient_mut){
distinct(reg_id, mut_id) %>%
count(reg_id, name = "n_mut")

# sort regions by number of covered patients
unique_reg <- unique_reg %>%
left_join(reg_to_n_patient, by = "reg_id") %>%
arrange(desc(n_patient)) %>%
mutate(
n_region = row_number(),
reg_size = reg_end - reg_start + 1,
reg_size_cum = cumsum(reg_size)
)

# cumulative number of patietns for each region
reg_to_n_patient_cum <- reg_to_patient_mut %>%
filter(!is.na(reg_id)) %>%
Expand Down