Checking if value in vector is in range of values in different length vector

bioinformatics, r

Solution

Using `dplyr`:

getValue <- function(x, data) {
  tmp <- data %>%
    filter(V2 <= x, x <= V3)
  return(tmp$V4)
}

x <- c(107599440, 150769180, 155204690)
sapply(x, getValue, data=df)

Which returns:

[1] "PRMT6" "CTSK"  "GBA"

Note: I copied your data into a dataframe `df` that has column names `V1`, `V2`, `V3`, and `V4`. The columns `V2` and `V3` are the lower and upper values of the range.

df <- read.table(text="chr1    100088228   100162167   AGL
chr1    107599438   107600565   PRMT6
chr1    115215635   115238091   AMPD1
chr1    11850637    11863073    MTHFR
chr1    119958143   119965343   HSD3B2
chr1    144124628   144128902   HFE2
chr1    150769175   150779181   CTSK
chr1    154245300   154248277   HAX1
chr1    155204686   155210803   GBA
chr1    156084810   156108997   LMNA", stringsAsFactors=FALSE)

Update:

In case of multiple matches, this will return the first match:

getValue <- function(x, data) {
  tmp <- data %>%
    filter(V2 <= x, x <= V3) %>%
    filter(row_number() == 1)
  return(tmp$V4)
}

There are multiple ranking functions. Check out `?row_number` for more info.

Problem

So I'm working in R and have a large dataframe that contains a vector that has genome positions like such: ``` 2655180 2657176 2658869 ``` And a second dataframe that has a a range of positions and a gene like such: ``` chr1 100088228 100162167 AGL chr1 107599438 107600565 PRMT6 chr1 115215635 115238091 AMPD1 chr1 11850637 11863073 MTHFR chr1 119958143 119965343 HSD3B2 chr1 144124628 144128902 HFE2 chr1 150769175 150779181 CTSK chr1 154245300 154248277 HAX1 chr1 155204686 155210803 GBA chr1 156084810 156108997 LMNA ``` Where the second and third columns are the start and end of the gene respectively. What I want to do is check if a row in the first data frame fits within the range of the second data frame and if so add the gene (column 4 of the second data frame) to the first data frame. My current implementation uses nested for loops to check each entry in the first dataframe against all entries in the second dataframe. Are there any R functions that could help me with accomplishing this task? In short: I need to check if a value in a row in a first vector is within a range specified in a differently sized second vector and then extract a value from the second vector.

Original source

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