我有两个Granges对象，我希望将它们合并以合并两个GRanges，即使两个对象中都不存在元数据。
> t
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | pvalue qvalue meth.diff gc.X gc.score
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <GRanges> <numeric>
[1] MT [ 708, 708] + | 2.898639e-04 0.007018699 0.2231039 MT:706-710 80
[2] MT [1147, 1147] - | 6.043240e-05 0.003882324 0.2243177 MT:1146-1150 80
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> s
GRanges object with 1 range and 6 metadata columns:
seqnames ranges strand | pvalue qvalue meth.diff gc.X gc.name gc.score
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <GRanges> <character> <numeric>
[1] MT [708, 708] + | 0.0002898639 0.007018699 0.2231039 MT:708:+ rs28412942 0
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
我想在结尾处：
> combined
GRanges object with 2 ranges and 5 metadata columns:
seqnames ranges strand | pvalue qvalue meth.diff gc.X gc.score gc.name
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <GRanges> <numeric>
[1] MT [ 708, 708] + | 2.898639e-04 0.007018699 0.2231039 MT:706-710 80 rs28412942
[2] MT [1147, 1147] - | 6.043240e-05 0.003882324 0.2243177 MT:1146-1150 80 NA
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
我尝试过的所有方法都要求具有相同的列数。 我可以尝试创建所需的列并用NA填充，但在我看来有点矫kill过正，我确定一种方法存在，但我找不到它：/
谢谢！
答案 0 :(得分：0)
使用findOverlaps
library(GenomicRanges)
m <- findOverlaps(s, t)
# Add gc.name to subject GRanges (i.e. left join)
mcols(t)$gc.name <- NA
mcols(t)[subjectHits(m), "gc.name"] = mcols(s)[queryHits(m), "gc.name"]
t
#GRanges object with 2 ranges and 6 metadata columns:
# seqnames ranges strand | pvalue qvalue meth.diff gc.X
# <Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric> <character>
# [1] MT [ 708, 708] + | 0.3361535 0.06058539 0.4743142 a
# [2] MT [1147, 1147] - | 0.4637233 0.19743361 0.3010486 b
# gc.score gc.name
# <numeric> <character>
# [1] 80 rs28412942
# [2] 80 <NA>
# -------
# seqinfo: 1 sequence from an unspecified genome; no seqlengths
set.seed(2018)
t <- GRanges(
seqnames = c("MT", "MT"),
IRanges(start = c(708, 1147), end = c(708, 1147)),
strand = c("+", "-"),
pvalue = runif(2),
qvalue = runif(2),
meth.diff = runif(2),
gc.X = letters[1:2],
gc.score = rep(80, 2))
set.seed(2018)
s <- GRanges(
seqnames = "MT",
IRanges(start = 708, end = 708),
strand = "+",
pvalue = runif(1),
qvalue = runif(1),
meth.diff = runif(1),
gc.X = letters[3],
gc.name = "rs28412942",
gc.score = 0)