How do you find the overlapping coordinates and extract the respective seg.mean values for the overlapping region?
data1
Rl pValue chr start end CNA
2 2.594433 6 129740000 129780000 gain
2 3.941399 6 130080000 130380000 gain
1 1.992114 10 80900000 81100000 gain
1 7.175750 16 44780000 44920000 gain
data2
ID chrom loc.start loc.end num.mark seg.mean
8410 6 129750000 129760000 8430 0.0039
8410 10 80907000 81000000 5 -1.7738
8410 16 44790000 44910000 12 0.0110
dataoutput
Rl pValue chr start end CNA seg.mean
2 2.594433 6 129750000 129760000 gain 0.0039
1 1.992114 10 80907000 81000000 gain -1.7738
1 7.175750 16 44790000 44910000 gain 0.0110
As we are working with genomics data it is easier to keep data as Granges objects, then we could use - mergeByOverlaps(g1,g2) from GenomicRanges package, see below example:
library("GenomicRanges")
#data
x1 <- read.table(text="Rl pValue chr start end CNA
2 2.594433 6 129740000 129780000 gain
2 3.941399 6 130080000 130380000 gain
1 1.992114 10 80900000 81100000 gain
1 7.175750 16 44780000 44920000 gain",header=TRUE)
x2 <- read.table(text="ID chrom loc.start loc.end num.mark seg.mean
8410 6 129750000 129760000 8430 0.0039
8410 10 80907000 81000000 5 -1.7738
8410 16 44790000 44910000 12 0.0110",header=TRUE)
g1 <- GRanges(seqnames=paste0("chr",x1$chr),
IRanges(start=x1$start,
end=x1$end),
CNA=x1$CNA,
Rl=x1$Rl)
g2 <- GRanges(seqnames=paste0("chr",x2$chrom),
IRanges(start=x2$loc.start,
end=x2$loc.end),
ID=x2$ID,
num.mark=x2$num.mark,
seq.mean=x2$seg.mean)
mergeByOverlaps(g1,g2)
# DataFrame with 3 rows and 7 columns
# g1 CNA Rl g2 ID num.mark seq.mean
# <GRanges> <factor> <integer> <GRanges> <integer> <integer> <numeric>
# 1 chr6:*:[129740000, 129780000] gain 2 chr6:*:[129750000, 129760000] 8410 8430 0.0039
# 2 chr10:*:[ 80900000, 81100000] gain 1 chr10:*:[ 80907000, 81000000] 8410 5 -1.7738
# 3 chr16:*:[ 44780000, 44920000] gain 1 chr16:*:[ 44790000, 44910000] 8410 12 0.0110
EDIT: Added sessionInfo() output:
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.20.3 GenomeInfoDb_1.4.0 IRanges_2.2.1 S4Vectors_0.6.0 BiocGenerics_0.14.0
[6] BiocInstaller_1.18.1
loaded via a namespace (and not attached):
[1] XVector_0.8.0 tools_3.2.0