我试图在granges对象中的元列的特定窗口上找到平均值。
所以我有一个数据对象：
> gr.data
GRanges object with 10505026 ranges and 1 metadata column:
seqnames ranges strand | value
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 [10468, 10468] + | 0
[2] chr1 [10469, 10469] - | 1
[3] chr1 [10470, 10470] + | 0.5
[4] chr1 [10471, 10471] - | 1
[5] chr1 [10483, 10483] + | 0.6
和一个窗口对象：
gr.windows
GRanges object with 6077 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [ 1, 100000] *
[2] chr1 [100001, 200000] *
[3] chr1 [200001, 300000] *
[4] chr1 [300001, 400000] *
[5] chr1 [400001, 500000] *
i然后将数据对象转换为rlelist：
gr.RleList <- mcolAsRleList(gr.data, varname = "value")
gr.RleList
RleList of length 3
$chr1
numeric-Rle of length 249239887 with 5816335 runs
Lengths: 10467 1 1 1 ... 1 1 13 2
Values : NA 0 1 0.5 ... 0 NaN NA NaN
如果然后使用binnedaverage，我只会得到na值。
gr.binnedAvg <- binnedAverage(gr.windows, gr.RleList, "value")
gr.binnedAvg
GRanges object with 6077 ranges and 1 metadata column:
seqnames ranges strand | value
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 [ 1, 100000] * | <NA>
[2] chr1 [100001, 200000] * | <NA>
[3] chr1 [200001, 300000] * | <NA>
[4] chr1 [300001, 400000] * | <NA>
[5] chr1 [400001, 500000] * | <NA>
unique(mcols(gr.binnedAvg)$value)
[1] NA
我还试图总结值，结果相同。我列表中的NA值弄乱了，还是我的侵犯中有问题？
最小示例：
library(BSgenome.Hsapiens.UCSC.hg19)
library(data.table)
gr.windows <- tileGenome(seqinfo(Hsapiens), tilewidth=100000,cut.last.tile.in.chrom=TRUE)
gr.data <- GRanges(c("chr1", "chr2"), IRanges(c(10, 50), c(15, 55)), value = c(20, 10))
gr.data.RleList <- mcolAsRleList(gr.data, varname = "value")
seqlevels(gr.windows, force=TRUE) <- names(gr.data.RleList)
gr.data.binnedAvg <- binnedAverage(gr.windows, gr.data.RleList, "value")
gr.data.binnedAvg
GRanges object with 4925 ranges and 1 metadata column:
seqnames ranges strand | value
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 [ 1, 100000] * | <NA>
[2] chr1 [100001, 200000] * | 0
[3] chr1 [200001, 300000] * | 0
[4] chr1 [300001, 400000] * | 0
非常感谢您的帮助！
使用"最小示例"，以下工作：
library(BSgenome.Hsapiens.UCSC.hg19)
library(GenomicRanges)
gr.windows <- tileGenome(seqinfo(Hsapiens), tilewidth=100000, cut.last.tile.in.chrom=TRUE)
gr.data <- GRanges(c("chr1", "chr2"), IRanges(c(10, 50), c(15, 55)), value=c(20, 10))
gr.data.cov <- GenomicRanges::coverage(gr.data, weight="value")
seqlevels(gr.windows, pruning.mode="coarse") <- names(gr.data.cov)
gr.data.binnedAvg <- binnedAverage(gr.windows, gr.data.cov, "value")
较晚的响应，但对于将来参考可能很有用。