Question

我有两个数据框：一个包含一个SNP及其位置的列表，另一个包含一个基因及其起始和结束坐标的列表。 使用dplyr ，我想在SNP数据框中添加一列，其名称为每个SNP所属的基因的名称（即SNP的位置在同一染色体上，并且位于基因的开始/结束坐标（含）。

如果SNP不在任何基因坐标内，则应在“基因”列中获得“ NA”。 SNP和基因之间的染色体数必须匹配。例如，即使第二个SNP的位置落在Gene4的开始/结束坐标之内，但这也不匹配，因为它们位于不同的染色体上。

SNP数据框：

CHR  POS  REF  ALT
01   5    C    T
01   10   G    A
02   5    G    T
02   15   C    A
02   20   T    C
03   10   A    G
03   20   C    T

GENE数据框：

CHR  START  END  GENE_NAME
01   2      8    Gene1
01   12     20   Gene2
01   25     30   Gene3
02   10     18   Gene4
02   25     35   Gene5
03   5      15   Gene6

所需的输出：

CHR  POS  REF  ALT  GENE_NAME
01   5    C    T    Gene1
01   10   G    A    NA
02   5    G    T    NA
02   15   C    A    Gene4
02   20   T    C    NA
03   10   A    G    Gene6
03   20   C    T    NA

同样，我想使用dplyr完成此操作。预先感谢您的帮助！

Answer 1

使用purrr中的GENE的一个选项是根据POS和CHR中的SNP过滤GENE_NAME数据帧，然后选择相应的library(dplyr) library(purrr) SNP %>% mutate(GENE_NAME = map2_chr(POS, CHR, function(x, y) { inds = x >= GENE$START & x <= GENE$END & y == GENE$CHR if (any(inds)) GENE$GENE_NAME[which.max(inds)] else NA })) # CHR POS REF ALT GENE_NAME #1 1 5 C T Gene1 #2 1 10 G A <NA> #3 2 5 G T <NA> #4 2 15 C A Gene4 #5 2 20 T C <NA> #6 3 10 A G Gene6 #7 3 20 C T <NA>。

mapply

在基数R中，可以使用mapply(function(x, y) { inds = x >= GENE$START & x <= GENE$END & y == GENE$CHR if (any(inds)) GENE$GENE_NAME[which.max(inds)] else NA }, SNP$POS, SNP$CHR) #[1] "Gene1" NA NA "Gene4" NA "Gene6" NA

编写

SNP <- structure(list(CHR = c(1L, 1L, 2L, 2L, 2L, 3L, 3L), POS = c(5L, 
10L, 5L, 15L, 20L, 10L, 20L), REF = c("C", "G", "G", "C", "T", 
"A", "C"), ALT = c("T", "A", "T", "A", "C", "G", "T")), class = 
"data.frame", row.names = c(NA, -7L))

GENE <- structure(list(CHR = c(1L, 1L, 1L, 2L, 2L, 3L), START = c(2L, 
12L, 25L, 10L, 25L, 5L), END = c(8L, 20L, 30L, 18L, 35L, 15L), 
GENE_NAME = c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5", 
"Gene6")), class = "data.frame", row.names = c(NA, -6L))

数据

{{1}}

Answer 2

这是使用class ViewController: UIViewController { @IBOutlet weak var level_Battery: UILabel! override func viewDidLoad() { super.viewDidLoad() UIDevice.current.isBatteryMonitoringEnabled = true let level = UIDevice.current.batteryLevel let battery_Level = Int(level * 100) level_Battery.text = "\(battery_Level)%" } }的一种方法。您只需扩展基于dplyr和gene的{{1}}数据帧，然后使用START-{p>扩展END

left_join

Answer 3

这是将Public Function Levenshtein(s1 As String, s2 As String) Dim i As Integer, j As Integer Dim l1 As Integer, l2 As Integer Dim min1 As Integer, min2 As Integer Dim d() As Integer 'For debugging purposes only Cells.Clear Dim rngOutput As Range: Set rngOutput = ActiveSheet.Range("A1").Resize(Len(s1) + 2, Len(s2) + 2) With rngOutput .ColumnWidth = 3 .HorizontalAlignment = xlCenter .VerticalAlignment = xlCenter End With l1 = Len(s1): l2 = Len(s2): ReDim d(l1, l2) For i = 0 To l1 d(i, 0) = i With rngOutput .Cells(i + 3, 1) = Mid(s1, i + 1, 1) If Not i = 0 Then .Cells(i + 2, 2) = i End With Next i For j = 0 To l2 d(0, j) = j With rngOutput .Cells(1, j + 3) = Mid(s2, j + 1, 1) If Not j = 0 Then .Cells(2, j + 2) = j End With Next j For i = 1 To l1 For j = 1 To l2 If Mid(s1, i, 1) = Mid(s2, j, 1) Then d(i, j) = d(i - 1, j - 1) With rngOutput.Cells(i + 2, j + 2) .Value = d(i, j) .Font.Color = vbBlue End With Else min1 = d(i - 1, j) + 1 min2 = d(i, j - 1) + 1 If min2 < min1 Then min1 = min2 End If min2 = d(i - 1, j - 1) + 1 If min2 < min1 Then min1 = min2 End If d(i, j) = min1 With Cells(i + 2, j + 2) .Value = d(i, j) .Font.Color = vbRed End With End If Next Next Levenshtein = d(l1, l2) End Function与non-equi结合使用的一种选择

data.table

或与library(data.table) setDT(snp)[gene, GENE_NAME := GENE_NAME, on = .(CHR, POS >= START, POS <= END)] snp # CHR POS REF ALT GENE_NAME #1: 1 5 C T Gene1 #2: 1 10 G A <NA> #3: 2 5 G T <NA> #4: 2 15 C A Gene4 #5: 2 20 T C <NA> #6: 3 10 A G Gene6 #7: 3 20 C T <NA>

fuzzyjoin

或带有library(fuzzyjoin) library(dplyr) fuzzy_left_join(snp, gene, by = c("CHR", "POS" = "START", "POS" = "END"), match_fun = list(`==`, `>=`, `<=`)) %>% select(CHR = CHR.x, POS, REF, ALT, GENE_NAME) # CHR POS REF ALT GENE_NAME #1 1 5 C T Gene1 #2 1 10 G A <NA> #3 2 5 G T <NA> #4 2 15 C A Gene4 #5 2 20 T C <NA> #6 3 10 A G Gene6 #7 3 20 C T <NA>的选项

rap

数据

library(rap)
snp %>% 
   rap(GENE_NAME = ~ filter(gene, CHR ==  !!CHR, START <= POS, END >= POS) %>% 
          pull(GENE_NAME)) %>% 
   mutate(GENE_NAME = replace(GENE_NAME, !lengths(GENE_NAME), NA)) %>% 
   unnest
#  CHR POS REF ALT GENE_NAME
#1   1   5   C   T     Gene1
#2   1  10   G   A      <NA>
#3   2   5   G   T      <NA>
#4   2  15   C   A     Gene4
#5   2  20   T   C      <NA>
#6   3  10   A   G     Gene6
#7   3  20   C   T      <NA>

根据SNP位置和基因开始/结束坐标从另一个数据框中分配基因名称

3 个答案:

数据