Question

我有一个数据集，我试图按1列（rssnp1列）中的重复ID进行排序，但是我只能找到重复函数来在线删除重复项。

我的数据如下：

Chr  Start   End     rssnp1        Type    gene
1   1244733 1244734 rs2286773   LD_SNP  ACE
1   1257536 1257436 rs301159    LD_SNP  CPEB4
1   1252336 1252336 rs2286773   Sentinel    CPEB4
1   1252343 1252343 rs301159    LD_SNP  CPEB4
1   1254841 1254841 rs301159    LD_SNP  CPEB4
1   1256703 1267404 rs301159    LD_SNP  CPEB4
1   1269246 1269246 rs301159    LD_SNP  CPEB4
1   1370168 1370168 rs301159    LD_SNP  GLUPA1
1   1371824 1371824 rs301159    LD_SNP  GLUPA1
1   1372591 1372591 rs301159    LD_SNP  GLUPA1

我的输出目标是：

Chr  Start   End     rssnp1        Type    gene
1   1244733 1244734 rs2286773   LD_SNP  ACE
1   1252336 1252336 rs2286773   Sentinel    CPEB4
1   1257536 1257436 rs301159    LD_SNP  CPEB4
1   1252343 1252343 rs301159    LD_SNP  CPEB4
1   1254841 1254841 rs301159    LD_SNP  CPEB4
1   1256703 1267404 rs301159    LD_SNP  CPEB4
1   1269246 1269246 rs301159    LD_SNP  CPEB4
1   1370168 1370168 rs301159    LD_SNP  GLUPA1
1   1371824 1371824 rs301159    LD_SNP  GLUPA1
1   1372591 1372591 rs301159    LD_SNP  GLUPA1

要重现数据，请使用：

structure(list(Chr = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Start = c(1244733, 
1257536, 1252336, 1252343, 1254841, 1256703, 1269246, 1370168, 
1371824, 1372591), End = c(1244734, 1257436, 1252336, 1252343, 
1254841, 1267404, 1269246, 1370168, 1371824, 1372591), rssnp1 = c("rs2286773", 
"rs301159", "rs2286773", "rs301159", "rs301159", "rs301159", 
"rs301159", "rs301159", "rs301159", "rs301159"), Type = c("LD_SNP", 
"LD_SNP", "Sentinel", "LD_SNP", "LD_SNP", "LD_SNP", "LD_SNP", 
"LD_SNP", "LD_SNP", "LD_SNP"), gene = c("ACE", "CPEB4", "CPEB4", 
"CPEB4", "CPEB4", "CPEB4", "CPEB4", "GLUPA1", "GLUPA1", "GLUPA1"
)), .Names = c("Chr", "Start", "End", "rssnp1", "Type", "gene"
), row.names = c(NA, -10L), class = c("tbl_df", "tbl", "data.frame"
))

我已经尝试过：

target_order <- c("a", "b", "c")
df[order(match(df$rssnp1)), target_order]

使用target_order中的每个唯一值而不是 c（“ a”，“ b”，“ c”）-所以我得到了类似c（“ rs2286773”，“ rs301159” ...）之类的东西，它可以用于我拥有的数百个ID。但这会导致错误：

Error in `[.data.frame`(df, order(match(df$rssnp1)), target_order) : 
  undefined columns selected

还有其他方法可以做到吗？

编辑： target_order需要位于代码的不同部分： df[order(match(df$rssnp1, target_order)), ]

但是，对于我来说，这仍然是一个乏味的工作方式-是否有更有效的方法来按重复进行排序？

Answer 1

根据我对您的描述的理解，您希望结果遵循 target_order 在其他地方计算出的特定顺序。这应该可以通过合并操作来完成。

假设您有以下顺序。

target_order<-c("rs301159", "rs2286773") 

dt <- structure(list(Chr = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Start = c(1244733, 
    1257536, 1252336, 1252343, 1254841, 1256703, 1269246, 1370168, 
    1371824, 1372591), End = c(1244734, 1257436, 1252336, 1252343, 
    1254841, 1267404, 1269246, 1370168, 1371824, 1372591), rssnp1 = c("rs2286773", 
    "rs301159", "rs2286773", "rs301159", "rs301159", "rs301159", 
    "rs301159", "rs301159", "rs301159", "rs301159"), Type = c("LD_SNP", 
    "LD_SNP", "Sentinel", "LD_SNP", "LD_SNP", "LD_SNP", "LD_SNP", 
    "LD_SNP", "LD_SNP", "LD_SNP"), gene = c("ACE", "CPEB4", "CPEB4", 
    "CPEB4", "CPEB4", "CPEB4", "CPEB4", "GLUPA1", "GLUPA1", "GLUPA1"
    )), .Names = c("Chr", "Start", "End", "rssnp1", "Type", "gene"
    ), row.names = c(NA, -10L), class = c("tbl_df", "tbl", "data.frame"
    ))

下面的代码应该能够产生所需的内容。

library(data.table)

setDT(dt)

# Setting sort=FALSE to persist the order in target_order
merge(as.data.table(target_order), dt, by.y="rssnp1", by.x="target_order", sort=FALSE)

 #     target_order Chr   Start     End     Type   gene
 #  1:     rs301159   1 1257536 1257436   LD_SNP  CPEB4
 #  2:     rs301159   1 1252343 1252343   LD_SNP  CPEB4
 #  3:     rs301159   1 1254841 1254841   LD_SNP  CPEB4
 #  4:     rs301159   1 1256703 1267404   LD_SNP  CPEB4
 #  5:     rs301159   1 1269246 1269246   LD_SNP  CPEB4
 #  6:     rs301159   1 1370168 1370168   LD_SNP GLUPA1
 #  7:     rs301159   1 1371824 1371824   LD_SNP GLUPA1
 #  8:     rs301159   1 1372591 1372591   LD_SNP GLUPA1
 #  9:    rs2286773   1 1244733 1244734   LD_SNP    ACE
 # 10:    rs2286773   1 1252336 1252336 Sentinel  CPEB4

如何按R中的重复项排序数据？

1 个答案: