R: Extract Rows from One Data Frame, Based on Column Names Matching Values from Another Data Frame

Question

I would like to know how to extract the values in one column of a data frame (data frame A) based on certain column names in data frame A containing the values of multiple columns from another data frame (data frame B) .

More specifically. I have two data frames:

Data frame A contains combinations of birth defects. Each row is a different combination, and each column is the number of a defect included in that combination.

# Combinations data frame 
combos <- data.frame("combo_no"=c(1:4),
                     "Defect_A" = c(1,1,1,1),
                     "Defect_B" = c(3,2,3,4),
                     "Defect_C" = c(4,4,NA,7),
                     "Defect_D" = c(5,5,NA,8),
                     "Defect_E" = c(6,6,NA,NA))

Data frame B contains individual cases. The first column has a unique identifier (CASE_ID). The rest of the columns are the numbers of specific birth defects, with “1” for “birth defect present” and “0” for “not present.”

# Cases data set 
set.seed(99)
CASE_ID = c(1001:1005)
case1 = sample(0:1, 10, replace=TRUE)  
case2 = sample(0:1, 10, replace=TRUE)  
case3 = sample(0:1, 10, replace=TRUE)  
case4 = sample(0:1, 10, replace=TRUE)  
case5 = sample(0:1, 10, replace=TRUE)  
def<-data.frame(rbind(case1, case2, case3, case4, case5))
colnames(def)<- c(1:10)
cases<-cbind(CASE_ID,def)

Desired Output: I would like to obtain the list of CASE_IDs from data frame A that have a combination of birth defects from data frame B. I'd also like to specify which combination is present. Ideally, the output would look as follows:

# Desired Output
output <- data.frame("CASE_ID" = c(1002,1003),
                     "combo_no" = c(3,1))

Thank you for your help.

Answer 1

Here the solution, long in order to comment it step by step:

### my random generated cases DF:
cases
      CASE_ID 1 2 3 4 5 6 7 8 9 10
case1    1001 1 0 1 1 1 1 1 0 0  0
case2    1002 1 1 0 1 1 1 0 0 0  0
case3    1003 0 0 1 1 1 0 0 1 0  0
case4    1004 1 0 0 1 0 0 1 1 1  1
case5    1005 1 0 1 1 0 1 0 0 1  0

### initialize vectors to store found results
found_combos <- vector(); found_patients <- vector();
### open loop on combos rows
for (i in 1:nrow(combos)) {
  ### open empty vector to fill with the numbers that compose the defect
  defect_numbers <- vector()
  ### open loop on column and take the numbers
  for (col in colnames(combos)[2:length(colnames(combos))]) {
    number <- combos[i, col]
    if ( !is.na(number) ) defect_numbers <- append(defect_numbers, number)
  }
  ### sort the vector to avoid mismatch based on order
  defect_numbers <- sort( defect_numbers )
  ### open loop on patients table
  for ( pz in 1:nrow(cases) ) {
    pz_numbers <- sort( which( cases[pz,] == 1 )-1 )
    ### first condition: same length
    if ( length(pz_numbers) == length(defect_numbers) ) {
      ### same condition: exacly same numbers
      if (all(pz_numbers == defect_numbers)) {
        ### append to found results vectors
        found_patients <- append( found_patients, cases[pz,1] )
        found_combos <- append( found_combos, i )
      }
    }
  }
}

output <- data.frame("CASE_ID" = found_patients,
                     "combo_no" = found_combos)

### result:
output
  CASE_ID combo_no
1    1002        2

---

EDITED based on your comment:

just change the conditions from equals to %in% :

### initialize vectors to store found results
found_combos <- vector(); found_patients <- vector();
for (i in 1:nrow(combos)) {
  ### open empty vector to fill with the numbers that compose the defect
  defect_numbers <- vector()
  ### open loop on column and take the numbers
  for (col in colnames(combos)[2:length(colnames(combos))]) {
    number <- combos[i, col]
    if ( !is.na(number) ) defect_numbers <- append(defect_numbers, number)
  }
  ### sort the vector to avoid mismatch based on order
  defect_numbers <- sort( defect_numbers )
  ### open loop on patients table
  for ( pz in 1:nrow(cases) ) {
    pz_numbers <- sort( which( cases[pz,] == 1 )-1 )
    ### only condition: all defect_numbers in combo_numbers vector
    if (all(defect_numbers %in% pz_numbers)) {
      ### append to found results vectors
      found_patients <- append( found_patients, cases[pz,1] )
      found_combos <- append( found_combos, i )
    }
  }
}

output <- data.frame("CASE_ID" = found_patients,
                     "combo_no" = found_combos)