I have mass spec data that I need help annotating. I have two files loaded. File1 has two columns (mz, intensity) and File2 has two as well (mz, name). In both files, all of the columns are numeric values, except for name that's characters. I need to take the mz value in File1 and match against the mz values in File2 within /- 0.001. If a value falls within that range in File1, I need to annotate with the 'name' value in File2. Below is an example:

File1

File2

the idea is to get an output like this:

I tried using mutate and merge, but I'm not sure how to add the number range and use a conditional statement to make it work. I also tried data.table, but again, not sure how to adjust for a range.

CodePudding user response：

library(dplyr)

## The example data.
file1 <- tibble::tribble(
  ~mz, ~intensity,
  100.1234, 1234,
  134.5678, 7653,
  150.1234, 23463,
  176.5678, 12354,
)
file2 <- tibble::tribble(
  ~mz, ~name,
  100.1225, "name1",
  112.5678, "name2",
  150.1239, "name3",
  176.5665, "name4",
)

out <-
  file1 %>%
  mutate(approx = round(mz, 3)) %>%
  left_join(file2 %>% mutate(approx = round(mz, 3)) %>% select(-mz),
            by = "approx") %>%
  select(-approx)

## Note that the output differs because ?round follows IEC 60559, IEEE 754

CodePudding user response：

suppose you have two data.frames file1 and file2:

With dplyr you can do::

library(dplyr)
file1 %>% rowwise() %>% mutate(
      name = if(any(abs(file2$mz - mz)<0.001)) 
        file2$name[min(which(abs(file2$mz - mz)<0.001))] else "")