Merge by Range in R – Applying Loops

by

The GenomicRanges package in Bioconductor is designed for this type of operation. Read your data in with, e.g., read.delim so that

con <- textConnection("SNP     BP
rs064   12292
rs319   345367
rs285   700042")
snps <- read.delim(con, head=TRUE, sep="")

con <- textConnection("Gene    BP_start    BP_end
E613    345344      363401
E92     694501      705408
E49     362370      368340") ## missing trailing digit on BP_end??
genes <- read.delim(con, head=TRUE, sep="")

then create ‘IRanges’ out of each

library(IRanges)
isnps <- with(snps, IRanges(BP, width=1, names=SNP))
igenes <- with(genes, IRanges(BP_start, BP_end, names=Gene))

(pay attention to coordinate systems, IRanges expects start and end to be included in the range; also, end >= start expect for 0-width ranges when end = start – 1). Then find the SNPs (‘query’ in IRanges terminology) that overlap the genes (‘subject’)

olaps <- findOverlaps(isnps, igenes)

two of the SNPs overlap

> queryHits(olaps)
[1] 2 3

and they overlap the first and second genes

> subjectHits(olaps)
[1] 1 2

If a query overlapped multiple genes, it would have been repeated in queryHits (and vice versa). You could then merge your data frames as

> cbind(snps[queryHits(olaps),], genes[subjectHits(olaps),])
    SNP     BP Gene BP_start BP_end
2 rs319 345367 E613   345344 363401
3 rs285 700042  E92   694501 705408

Usually genes and SNPs have chromosome and strand (‘+’, ‘-‘, or ‘*’ to indicate that strand isn’t important) information, and you’d want to do overlaps in the context of these; instead of creating ‘IRanges’ instances, you’d create ‘GRanges’ (genomic ranges) and the subsequent book-keeping would be taken care of for you

library(GenomicRanges)
isnps <-
    with(snps, GRanges("chrA", IRanges(BP, width=1, names=SNP), "*")
igenes <-
    with(genes, GRanges("chrA", IRanges(BP_start, BP_end, names=Gene), "+"))

More Related Contents:

  1. Simultaneously merge multiple data.frames in a list
  2. Find complement of a data frame (anti – join)
  3. Compare two data.frames to find the rows in data.frame 1 that are not present in data.frame 2
  4. Loop in R to read many files
  5. Left join using data.table
  6. Merging a lot of data.frames [duplicate]
  7. Read all files in directory and apply multiple functions to each data frame [duplicate]
  8. Merge two data frames while keeping the original row order
  9. How to delete rows from a dataframe that contain n*NA
  10. Merge several data.frames into one data.frame with a loop
  11. Merge unequal dataframes and replace missing rows with 0
  12. Remove/collapse consecutive duplicate values in sequence
  13. Use merge() to update a data frame with values from a second data frame
  14. How to Loop/Repeat a Linear Regression in R
  15. R ggplot2 merge with shapefile and csv data to fill polygons
  16. Comparing two vectors in an if statement
  17. Cumulative sum until maximum reached, then repeat from zero in the next row
  18. Combine/merge lists by elements names
  19. Looping through t.tests for data frame subsets in r
  20. R assigning ggplot objects to list in loop
  21. Merge data frames based on rownames in R
  22. Breaking loop when “warnings()” appear in R
  23. Merging two columns into one in R [duplicate]
  24. R: merge two irregular time series
  25. Merge error : negative length vectors are not allowed
  26. Identify records in data frame A not contained in data frame B [closed]
  27. Efficiently merging two data frames on a non-trivial criteria
  28. How can I merge more than 2 dataframes in R by rownames?
  29. How can I merge many data frames from csv files when the ID column is implied?
  30. Merging multiple data.tables

Leave a Comment