GRangesオブジェクトをループするときにエラーが発生しました（エラーeval（expr、envir、enclos）：非機能を適用しようとしました）

Question

私は2つのデータセットを持っています：GRACesオブジェクトとして1つはGRangesListで複数のサブセットもう1つ（テスト）。 grlのすべてのサブセットをループし、 "GenomicRanges"ライブラリのfindOverlaps関数を使用して、その重複をTestとし、リスト内のデータ（各反復後に1つの値のみ）を保存したいとします。

出力は次のようになります。

gr1 2 
gr2 5 
gr3 1 


gr1 <- 
    GRanges(seqnames = "chr2", ranges = IRanges(3, 6), 
      strand = "+", score = 5L, GC = 0.45) 
gr2 <- 
    GRanges(seqnames = c("chr1", "chr1"), 
      ranges = IRanges(c(7,13), width = 3), 
      strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5)) 
gr3 <- 
    GRanges(seqnames = c("chr1", "chr2"), 
      ranges = IRanges(c(1, 4), c(3, 9)), 
      strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1)) 
grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3) 
grl 


Test <- 
    GRanges(seqnames = c("chr1", "chr1"), 
      ranges = IRanges(c(1, 5), c(2, 6)), 
      strand = c("-", "-"), score = c(6L, 2L), GC = c(0.5, 0.2)) 


myFunction <- function(input,feature){ 

    tmp = list() 

     for (f in 1:length(objects(feature))){ 

      mtch = findOverlaps(currmySegm, eval(parse(text=paste0("feature$", objects(feature[f]), sep = ""))))) 
      **some calculations** 
      value <- mean(...) 
      } 
     temp[[objects(feature[f])]] <- value 
} 

myFunction(Test,grl) 

Error in eval(expr, envir, enclos) : attempt to apply non-function 

私は機能findOverlapsにgrlのサブセットを渡すか、またはリスト

Answer 1

として結果を保存することはできません eval(parse(text=paste0("feature$", objects(feature[f]), sep = ""))))に何か問題のいずれかがあると思います

異なるfindOverlaps例：

# GRangesList object 
gr1 <- 
    GRanges(seqnames = "chr2", ranges = IRanges(3, 6), 
      strand = "+", score = 5L, GC = 0.45) 
gr2 <- 
    GRanges(seqnames = c("chr1", "chr1"), 
      ranges = IRanges(c(7,13), width = 3), 
      strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5)) 
gr3 <- 
    GRanges(seqnames = c("chr1", "chr2"), 
      ranges = IRanges(c(1, 4), c(3, 9)), 
      strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1)) 
grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3) 


# GRanges object 
Test <- 
    GRanges(seqnames = c("chr1", "chr1"), 
      ranges = IRanges(c(1, 5), c(2, 6)), 
      strand = c("-", "-"), score = c(6L, 2L), GC = c(0.5, 0.2)) 

# Get overlaps at the GRanges entry level of a GRangesList object 
# This extracts the overlapping GRanges entries from your grl 
# GRangesList object that overlap with a feature from Test. 
hits1 <- lapply(grl, function(x) findOverlaps(x, Test)); 
grl.overlapping <- list(); 
for (i in 1:length(hits1)) { 
    grl.overlapping[[i]] <- grl[[i]][queryHits(hits1[[i]])]; 
} 
names(grl.overlapping) <- names(grl); 
print(grl.overlapping); 

# Count the number of overlapping GRanges objects for every 
# list entry from grl 
counts <- lapply(hits1, length); 
print(counts); 

# Get overlaps at the GRangesList level 
# Note this will only tell you whether *any* GRanges entries from your 
# grl GRangesList object overlap with a feature from Test; it won't 
hits2 <- findOverlaps(grl, Test); 
print(grl[queryHits(hits2)]);