如何根据 R 中另一个文件的多个条件 select 行文件？

Question

我有 2 个遗传数据集。我根据 file2 中的列过滤 file1。但是，我还需要考虑 file2 中的第二列，但我不确定该怎么做。

文件 1 行提取的条件是，仅选择染色体位置比文件 2 中同一染色体上的任何染色体位置大 5000 以上或小 5000 以上的行。

例如我的数据如下：

文件 1：

Variant   Chromsome   Chromosome Position  
Variant1      2             14000     
Variant2      1             9000              
Variant3      8             37000          
Variant4      1             21000

文件 2：

Variant  Chromosome  Chromosome Position  
Variant1     1                 10000                   
Variant2     1                 20000                   
Variant3     8                 30000

预期输出（与同一染色体上文件 2 的任何行相比，位置距离大于 +/-5000 的变体）：

Variant   Chromosome Position     Chromosome
Variant1    14000                  2
Variant3    37000                  8

#Variant1 at 14000, whilst within 5000 + of Variant1 at 10000 in file2 is on a different chromosome and therefore not compared and is kept.
#Variant3 is on the same chromosome as Variant4 in file1 but larger than 5000+ distance and is kept.

我试过使用 unix 编码，但是在没有考虑染色体的情况下，每个变体只能得到大于 5000 +/- 的过滤，并且被建议尝试在 R 中编码，但是我是 R 的新手而且我是不知道从哪里开始。我假设我需要一个 "if line of file1 has matching chromosome number as file2, then perform the larger than 5000 +/- filtering within that chromosome number only" 的 if 语句和一个用于遍历每一行的 for 循环 - 即使只是关于如何学习如何做到这一点的指导也会受到赞赏。

Answer 1

使用您的示例数据和方法，我想出了这个 data.table-解决方案

代码中注释了一个简短的解释。

library( data.table)
#sample data
dt1 <- fread("Variant   Chromosome   Chromosome_Position  
Variant1      2             14000     
Variant2      1             9000              
Variant3      8             37000          
Variant4      1             21000")
dt2 <- fread("Variant  Chromosome  Chromosome_Position  
Variant1     1                 10000                   
Variant2     1                 20000                   
Variant3     8                 30000")

#create lower&upper boundaries for dt2 chromosome position
dt2[, c("low", "high") := .(Chromosome_Position - 5000, Chromosome_Position + 5000)]
#dt2 now looks like this:
#-------------------------------------------------------------
#     Variant Chromosome Chromosome_Position   low  high
# 1: Variant1          1               10000  5000 15000
# 2: Variant2          1               20000 15000 25000
# 3: Variant3          8               30000 25000 35000

#find matches on chromosome, with position bewtene low-high
#  this is done using a non-equi join using the lower and upper boundaries
#  created in dt2 in the previous line.
#  on = .(...) means: Chromosome in dt1 and dt2 have to be the same
#                     Chromosome_Position in dt1 has to be between 
#                       low and high of dt2. Y
#                       You can (of course) use >= and <= if desired.
#  match := i.Variant creates a new column in dt1, with the value of
#                     Variant from dt2 (if a match is found).
#                     If no match is found, the columns gets a <NA>.                          
dt1[ dt2, match := i.Variant,
     on = .(Chromosome, Chromosome_Position > low, Chromosome_Position < high ) ]
#dt1 now looks like this
#see the match-column for found dt1-matches in dt2
#-------------------------------------------------------------
#     Variant Chromosome Chromosome_Position    match
# 1: Variant1          2               14000     <NA>
# 2: Variant2          1                9000 Variant1
# 3: Variant3          8               37000     <NA>
# 4: Variant4          1               21000 Variant2

#discard all found matches (i.e. is.na(Match) == TRUE), and drop match-column,
#  since we no longer need it.
dt1[ is.na(match) ][, match := NULL ][]

#     Variant Chromosome Chromosome_Position
# 1: Variant1          2               14000
# 2: Variant3          8               37000

如何根据 R 中另一个文件的多个条件 select 行文件？

How to select lines of file based on multiple conditions of another file in R?

r

bioinformatics

conditional-statements