任何方式强制 "list" 到 S4 "List"？
Any way coercing "list" to S4 "List"?
有没有办法将简单的类列表对象强制转换为 S4 "List" 对象？我需要对我的数据进行一些矢量化。显然，我在我的函数中使用了 nested-lapply，并且我检查它的 return 类型为 "list"。我想要 "List" 之类的对象。我怎样才能做到这一点？谢谢。
这是澄清问题的可重现示例：
数据
foo <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3", "chr4"), c(3, 2, 1, 2)),
ranges=IRanges(seq(1, by=9, len=8), seq(7, by=9, len=8)),
rangeName=letters[seq(1:8)], score=sample(1:20, 8, replace = FALSE))
bar <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3","chr4"), c(4, 3, 1, 1)),
ranges=IRanges(seq(2, by=5, len=9), seq(4, by=5, len=9)),
rangeName=letters[seq(1:9)], score=sample(1:20, 9, replace = FALSE))
moo <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3","chr4"), c(3, 4, 2,1)),
ranges=IRanges(seq(5, by=7, len=10), seq(8, by=7, len=10)),
rangeName=letters[seq(1:10)], score=sample(1:20, 10, replace = FALSE))
重叠命中指数
grl <- GRangesList(bar, moo)
res <- lapply(grl, function(ele_) {
tmp <- as(findOverlaps(foo, ele_), "List")
})
重复区域的解释（第一个列表元素对应于条）：
[[1]]
IntegerList of length 8
[[1]] 1 2 # 1st regions from foo overlapped with 1st,2nd regions from bar
[[2]] 3
[[3]] 4
[[4]] 6 7 # 1st regions from foo overlapped with 6st,7th regions from bar
objective只保留一个（a.k.a，去掉多个相交的区域），如：
[[1]]
IntegerList of length 8
[[1]] 2 # only keep 2nd region from bar
[[2]] 3
[[3]] 4
[[4]] 6 7 # only keep 6th region from bar
删除重复区域
obj.ov <- lapply(res, function(ele_) {
re <- lapply(grl, function(obj) {
id0 <- as(which.max(extractList(obj$score, ele_)), "List")
id0 <- id0[!is.na(id0)]
})
re <- re[!duplicated(re)]
})
进一步的步骤
as.obj.ov <- as(obj.ov, "List") # 如果这个强制转换不对，就不能像 obj.ov
一样展开
那么，as.obj.ov 必须像 obj.ov 一样可扩展为命中索引向量，也类型必须是 S4 "List" 对象。
我需要让 obj.ov 作为 S4 "List" 对象。可以在 R 中进行这种强制转换吗？
感谢任何可能的方法、解决方案或想法。
我们可以使用 select = "first" 来获得第一个匹配项。
lapply(grl, function(ele_) {
ix <- findOverlaps(foo, ele_, select = "first")
ele_[ix[!is.na(ix)]]
})
[[1]]
GRanges object with 4 ranges and 2 metadata columns:
seqnames ranges strand | rangeName score
<Rle> <IRanges> <Rle> | <character> <integer>
[1] chr1 [ 2, 4] * | a 18
[2] chr1 [12, 14] * | c 2
[3] chr1 [17, 19] * | d 19
[4] chr2 [27, 29] * | f 15
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
[[2]]
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | rangeName score
<Rle> <IRanges> <Rle> | <character> <integer>
[1] chr1 [ 5, 8] * | a 11
[2] chr1 [12, 15] * | b 13
[3] chr1 [19, 22] * | c 14
[4] chr2 [26, 29] * | d 20
[5] chr2 [40, 43] * | f 8
[6] chr4 [68, 71] * | j 1
-------
seqinfo: 4 sequences from an unspecified genome; no seqlength
有没有办法将简单的类列表对象强制转换为 S4 "List" 对象？我需要对我的数据进行一些矢量化。显然，我在我的函数中使用了 nested-lapply，并且我检查它的 return 类型为 "list"。我想要 "List" 之类的对象。我怎样才能做到这一点？谢谢。
这是澄清问题的可重现示例：
数据
foo <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3", "chr4"), c(3, 2, 1, 2)),
ranges=IRanges(seq(1, by=9, len=8), seq(7, by=9, len=8)),
rangeName=letters[seq(1:8)], score=sample(1:20, 8, replace = FALSE))
bar <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3","chr4"), c(4, 3, 1, 1)),
ranges=IRanges(seq(2, by=5, len=9), seq(4, by=5, len=9)),
rangeName=letters[seq(1:9)], score=sample(1:20, 9, replace = FALSE))
moo <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr3","chr4"), c(3, 4, 2,1)),
ranges=IRanges(seq(5, by=7, len=10), seq(8, by=7, len=10)),
rangeName=letters[seq(1:10)], score=sample(1:20, 10, replace = FALSE))
重叠命中指数
grl <- GRangesList(bar, moo)
res <- lapply(grl, function(ele_) {
tmp <- as(findOverlaps(foo, ele_), "List")
})
重复区域的解释（第一个列表元素对应于条）：
[[1]]
IntegerList of length 8
[[1]] 1 2 # 1st regions from foo overlapped with 1st,2nd regions from bar
[[2]] 3
[[3]] 4
[[4]] 6 7 # 1st regions from foo overlapped with 6st,7th regions from bar
objective只保留一个（a.k.a，去掉多个相交的区域），如：
[[1]]
IntegerList of length 8
[[1]] 2 # only keep 2nd region from bar
[[2]] 3
[[3]] 4
[[4]] 6 7 # only keep 6th region from bar
删除重复区域
obj.ov <- lapply(res, function(ele_) {
re <- lapply(grl, function(obj) {
id0 <- as(which.max(extractList(obj$score, ele_)), "List")
id0 <- id0[!is.na(id0)]
})
re <- re[!duplicated(re)]
})
进一步的步骤
as.obj.ov <- as(obj.ov, "List") # 如果这个强制转换不对，就不能像 obj.ov
那么，as.obj.ov 必须像 obj.ov 一样可扩展为命中索引向量，也类型必须是 S4 "List" 对象。
我需要让 obj.ov 作为 S4 "List" 对象。可以在 R 中进行这种强制转换吗？
感谢任何可能的方法、解决方案或想法。
我们可以使用 select = "first" 来获得第一个匹配项。
lapply(grl, function(ele_) {
ix <- findOverlaps(foo, ele_, select = "first")
ele_[ix[!is.na(ix)]]
})
[[1]]
GRanges object with 4 ranges and 2 metadata columns:
seqnames ranges strand | rangeName score
<Rle> <IRanges> <Rle> | <character> <integer>
[1] chr1 [ 2, 4] * | a 18
[2] chr1 [12, 14] * | c 2
[3] chr1 [17, 19] * | d 19
[4] chr2 [27, 29] * | f 15
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
[[2]]
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | rangeName score
<Rle> <IRanges> <Rle> | <character> <integer>
[1] chr1 [ 5, 8] * | a 11
[2] chr1 [12, 15] * | b 13
[3] chr1 [19, 22] * | c 14
[4] chr2 [26, 29] * | d 20
[5] chr2 [40, 43] * | f 8
[6] chr4 [68, 71] * | j 1
-------
seqinfo: 4 sequences from an unspecified genome; no seqlength