On 01/18/2012 07:25 AM, rantree wrote:
I've got two tables....
first one(table1):
ID chrom start end
Ex1 2 152 180
Ex2 10 2000 2220
Ex3 15 3000 4000
second one ( table2):
chrom location name
2 160 Alv
2 190 GNN
2 100 ARg
10 210 GGG
15 3200 ADSA
What I have to do is to put name column in table1 when the location of
the name is between the start and end ....and chrom must be the same....it
will be this the result:
ID chrom start end name
Ex1 2 152 180 Alv
Ex2 10 2000 2220 GGG
Ex3 15 3000 4000 ADSA
How can i do this ????
Install the Bioconductor package GenomicRanges
source("http://bioconductor.org/biocLite.R";)
biocLite("GenomicRanges")
then
library(GenomicRanges)
t1 <- GRanges(c("2", "10", "15"),
IRanges(c(152, 2000, 3000),
c(180, 2220, 4000)),
Id=c("Ex1", "Ex2", "Ex3"))
t2 <- GRanges(c("2", "2", "2", "10", "15"),
IRanges(c(160, 190, 100, 2010, 3200),
width=1),
Name=c("Alv", "GNN", "ARg", "GGG", "ADSA"))
idx <- match(t1, t2)
values(t1)$Name <- values(t2)$Name[idx]
leading to
> t1
GRanges with 3 ranges and 2 elementMetadata values:
seqnames ranges strand | Id Name
<Rle> <IRanges> <Rle> | <character> <character>
[1] 2 [ 152, 180] * | Ex1 Alv
[2] 10 [2000, 2220] * | Ex2 GGG
[3] 15 [3000, 4000] * | Ex3 ADSA
---
seqlengths:
10 15 2
NA NA NA
> as.data.frame(t1)
seqnames start end width strand Id Name
1 2 152 180 29 * Ex1 Alv
2 10 2000 2220 221 * Ex2 GGG
3 15 3000 4000 1001 * Ex3 ADSA
and many other sequence-related operations.
Hope that helps,
Martin
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