Question

我有两个数据框

    A ### data frame contain GO ids

    GOBPID

    G0:00987
    GO:06723
    GO:02671
    GO:00654
    GO:00132

   B ### containing GO ids with their associated columns

    GOBPID    term

    GO:08765  flavonoid synthesis
    G0:00133  biosynthesis process
    G0:00987  carotenoid synthesis
    GO:06723  coumarin synthesis
    GO:00824  metabolic process
    GO:02671  leaf morphology
    GO:00654  response to light
    GO:00268  response to stress
    GO:00135  pathogen defense
    GO:00132  spindle formation

我想从A和B中仅提取公共ID并删除其余行

    #from A    # from B    # from B
    G0:00987   G0:00987    carotenoid synthesis
    GO:06723   GO:06723    coumarin synthesis
    GO:02671   GO:02671    leaf morphology
    GO:00654   GO:00654    response to light
    GO:00132   GO:00132    spindle formation

并做了以下事情：

  list of terms<- merge(A,B,by.x="GOBPID",by.y="GOBPID")

但是出现了错误并返回了一个0长度的数据帧，该数据帧只有列名但没有合并。

  [1] GOBPID        Term     
   <0 rows> (or 0-length row.names)

再次尝试以下

  merge(A,B,by.x="row.names",by.y="row.names")

只是合并了两个数据框，但没有给我公共ID。来自A的5个ID与B中的前5个ID匹配，并且不考虑仅合并常见ID。

我也添加了两个数据集：

  [dataset A][http://public.justcloud.com/dldzm0fnsp.4540049] 
  [dataset B][http://public.justcloud.com/dldzmx1758.4540049]

Answer 1

只需使用标准数据帧子集：

R> dd_B[dd_B$GOBPID %in% dd_A$GOBPID,]
     GOBPID                label
3  G0:00987 carotenoid synthesis
4  GO:06723   coumarin synthesis
6  GO:02671      leaf morphology
7  GO:00654    response to light
10 GO:00132    spindle formation

%in%运算符会测试GOBPID中的B是否在A

我认为你不需要第一列，因为它只是中间列的副本

以上示例的代码：

dd_A = data.frame(GOBPID = c("G0:00987", "GO:06723", "GO:02671", "GO:00654", "GO:00132"))

dd_B = read.table(textConnection('GO:08765  "flavonoid synthesis"
G0:00133  "biosynthesis process"
G0:00987  "carotenoid synthesis"
GO:06723  "coumarin synthesis"
GO:00824  "metabolic process"
GO:02671  "leaf morphology"
GO:00654  "response to light"
GO:00268  "response to stress"
GO:00135  "pathogen defense"
GO:00132  "spindle formation"'))

colnames(dd_B) = c("GOBPID", "label")

dd_B[dd_B$GOBPID %in% dd_A$GOBPID,]

合并GO术语时出错 - 合并功能

1 个答案: