重复匹配

在 R 中使用 data.table 进行数据表连接

Scott Ritchie

Postdoctoral Researcher in Systems Genomics

连接键的重复项

# 使用任意方法，哪些细菌在两个站点都能找到？
site1_ecology[site2_ecology, on = .(genus)]

乘法式匹配导致的错误

site1_ecology[site2_ecology, on = .(genus)]


Error in vecseq(f__, len__, if (allow.cartesian || notjoin || 
!anyDuplicated(f__,  : 
  Join results in 12 rows; more than 10 = nrow(x)+nrow(i). Check for 
  duplicate key values in i each of which join to the same group in x over 
  and over again. If that's ok, try by=.EACHI to run j for each group to 
  avoid the large allocation. If you are sure you wish to proceed, rerun 
  with allow.cartesian=TRUE. Otherwise, please search for this error message 
  in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.

允许乘法式匹配

allow.cartesian = TRUE 允许继续执行连接：

# data.table 语法
site1_ecology[site2_ecology, on = .(genus), allow.cartesian = TRUE]

# merge()
merge(site1_ecology, site2_ecology, by = "genus", allow.cartesian = TRUE)

允许乘法式匹配

site1_ecology[site2_ecology, on = .(genus), allow.cartesian = TRUE]

           genus count method present i.method
 1: Nitrosomonas   500    WGS    TRUE      WGS
 2: Nitrosomonas   620    16S    TRUE      WGS
 3: Nitrosomonas   500    WGS    TRUE      16S
 4: Nitrosomonas   620    16S    TRUE      16S
 5: Nitrosomonas   500    WGS    TRUE  Culture
 6: Nitrosomonas   620    16S    TRUE  Culture
 7:    Rhizobium   360    WGS    TRUE      WGS
 8:    Rhizobium   300    16S    TRUE      WGS
 9:    Rhizobium   360    WGS    TRUE      16S
10:    Rhizobium   300    16S    TRUE      16S
11:    Rhizobium   360    WGS   FALSE  Culture
12:    Rhizobium   300    16S   FALSE  Culture

缺失值

缺失值（NA）会与其他缺失值匹配：

过滤缺失值

可用 !is.na() 过滤缺失值行

site1_ecology <- site1_ecology[!is.na(genus)]
site1_ecology

          genus count method
1: Nitrosomonas   500    WGS
2:    Rhizobium   360    WGS

site2_ecology <- site2_ecology[!is.na(genus)]
site2_ecology

          genus present  method
1: Nitrosomonas    TRUE Culture
2:    Rhizobium    TRUE Culture
3:  Azotobacter    TRUE Culture

仅保留首次匹配

site1_ecology[site2_ecology, on = .(genus), mult = "first"]

仅保留最后匹配

children[parents, on = .(parent = name), mult = "last"]

识别并移除重复项

duplicated()：哪些行是重复的？

unique()：将 data.table 过滤为唯一行

duplicated() 函数

使用所有列的取值：

duplicated(site1_ecology)

FALSE FALSE FALSE FALSE

仅使用部分列：

duplicated(site1_ecology, 
           by = "genus")

FALSE TRUE FALSE TRUE

unique() 函数

unique(site1_ecology, by = "genus")

更改搜索顺序

fromLast = TRUE 将搜索方向改为从最后一行开始

duplicated(site1_ecology, by = "genus", fromLast = TRUE)

TRUE FALSE TRUE FALSE

unique(site1_ecology, by = "genus", fromLast = TRUE)

开始练习吧！

在 R 中使用 data.table 进行数据表连接