Map snps into a ref gene file using R

[Marwah Soliman]

I have the following data set about the snps ID

   POS        ID	
    	78599583	rs987435
    	33395779	rs345783
    	189807684	rs955894
    	33907909	rs6088791
    	75664046	rs11180435
    	218890658	rs17571465
    	127630276	rs17011450
    	90919465	rs6919430

and a gene reference file

genename	name	chrom	strand	txstart	txend
    CDK1	NM_001786	chr10	+	62208217	62224616
    CALB2	NM_001740	chr16	+	69950116	69981843
    STK38	NM_007271	chr6	-	36569637	36623271
    YWHAE	NM_006761	chr17	-	1194583	1250306
    SYT1	NM_005639	chr12	+	77782579	78369919
    ARHGAP22	NM_001347736	chr10	-	49452323	49534316
    PRMT2	NM_001535	chr21	+	46879934	46909464
    CELSR3	NM_001407	chr3	-	48648899	48675352

I'm trying to match the genes with the SNps using snp location, so include the snps that has

POS >= txstart and POS<= txend

for example I want a data set that has the following columns

genename   SNPID   chrom   position   txstart   txend

how to do this match using R

 

[trinker]

Sounds like a filter and match or match and filter. Have you looked at the match function?

 

[Marwah Soliman]

No I haven't can you tell me what does it do

 

[trinker]

It merges files. There are examples in the help file at the bottom to help you Type ?merge into the command line for the help file. It gives the following:

## use character columns of names to get sensible sort order
authors <- data.frame(
    surname = I(c("Tukey", "Venables", "Tierney", "Ripley", "McNeil")),
    nationality = c("US", "Australia", "US", "UK", "Australia"),
    deceased = c("yes", rep("no", 4)))
books <- data.frame(
    name = I(c("Tukey", "Venables", "Tierney",
             "Ripley", "Ripley", "McNeil", "R Core")),
    title = c("Exploratory Data Analysis",
              "Modern Applied Statistics ...",
              "LISP-STAT",
              "Spatial Statistics", "Stochastic Simulation",
              "Interactive Data Analysis",
              "An Introduction to R"),
    other.author = c(NA, "Ripley", NA, NA, NA, NA,
                     "Venables & Smith"))

(m1 <- merge(authors, books, by.x = "surname", by.y = "name"))
(m2 <- merge(books, authors, by.x = "name", by.y = "surname"))
stopifnot(as.character(m1[, 1]) == as.character(m2[, 1]),
          all.equal(m1[, -1], m2[, -1][ names(m1)[-1] ]),
          dim(merge(m1, m2, by = integer(0))) == c(36, 10))

## "R core" is missing from authors and appears only here :
merge(authors, books, by.x = "surname", by.y = "name", all = TRUE)

## example of using 'incomparables'
x <- data.frame(k1 = c(NA,NA,3,4,5), k2 = c(1,NA,NA,4,5), data = 1:5)
y <- data.frame(k1 = c(NA,2,NA,4,5), k2 = c(NA,NA,3,4,5), data = 1:5)
merge(x, y, by = c("k1","k2")) # NA's match
merge(x, y, by = "k1") # NA's match, so 6 rows
merge(x, y, by = "k2", incomparables = NA) # 2 rows

 

[Marwah Soliman]

can you please suggest a code to solve this problem in R