This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Match values within a range from uneven data frames

Hello! Thank you for your help in advance.

I have two data frames DataBase and Hits

DataBase=
X  Y    OTDB
0   0    OTDB001
2  14   OTDB002
0   0.5  OTDB003 

Hits=
X   Y       Signal
0    0       100
2.1 14.3   20
7    15       90

Results=
X   Y    Signal  OTDB
0    0    100      OTDB001
0    0    100      OTDB003
2.1 14.3 20      OTDB002
7     15   90       NA

For every X, Y in Hits I want to search the database to see if there is a corresponding value within a threshold of X+/- 0.1 and Y+/- 0.5. If there is a value(s) that matches within the threshold I want to add the OTDB number or "NA" to a new column in a Results data frame. It is likely multiple dataBase entries will match an X,Y from the hits.

For perfect matches of X,Y between Database and Hits I used 

Results=merge(DataBase, Hits, by=c("X", "Y"), all.x = TRUE, all.y = TRUE)

However I'm having trouble setting the tolerance in searching. Thank you again for any advice!

r
• 2,058 views • link
updated by Biostar Biostar • written by odayel • odayel

1 answer

This is a way to do it (probably not the best):

# datasets.
db <- data.frame(
  x = c(0, 2, 0),
  y = c(0, 14, .5),
  otdb = c("OTDB001", "OTDB002", "OTDB003")
)
db
  x    y    otdb
1 0  0.0 OTDB001
2 2 14.0 OTDB002
3 0  0.5 OTDB003

hits <- data.frame(
  x = c(0, 2.1, 7),
  y = c(0, 14.3, 15),
  signal = c(100, 20, 90)
)
hits
    x    y signal
1 0.0  0.0    100
2 2.1 14.3     20
3 7.0 15.0     90

tol <- 0.5 # set tolerance.
# iterate over hits:
res <- lapply(seq_len(nrow(hits)), function(i) {
  h <- hits[i, ]
  sel.x <- db$x <= h$x + tol & db$x >= h$x - tol
  sel.y <- db$y <= h$y + tol & db$y >= h$y - tol
  sel <- sel.x & sel.y
  if (any(sel)) {
    data.frame(x = db$x[sel], y = db$y[sel], signal = h$signal, otdb = db$otdb[sel])
  } else {
    data.frame(x = h$x, y = h$y, signal = h$signal, otdb = NA)
  }
})
res <- do.call(rbind, res)
res
  x    y signal    otdb
1 0  0.0    100 OTDB001
2 0  0.5    100 OTDB003
3 2 14.0     20 OTDB002
4 7 15.0     90    <NA>
• 0 views • link
written by ddiez ddiez

Thank you! This works great! I really appreciate your help!! thank you again!

• 0 views • link
written by odayel • odayel

Log in to answer this question.

More posts like this