在R中基于另一个表过滤一个表

Question

I have one table(1) that looks like this (it is an all by all distance matrix transformed into a tab separated list):

sample1    sample2    405
sample3    sample4    400
sample5    sample6    1
sample7    sample8    20
sample1    sample3    40

I have another table(2) which contains those samples which meet a certain criteria:

sample1
sample2
sample8

How can I parse the first table(1) to extract only those rows in which both the variables in columns 1 and 2 can be found in table(2) ?

ie desired comparisons are only:

sample1    sample2    405
sample2    sample8    40
sample8    sample1    100

Answer 1

I tried a similar set-up using a dataframe for your table(1) and a vector for your table(2).

table_one <- data.frame(col_1 = c("a", "b", "c", "d"),
       col_2 = c("b", "d", "f", "g"),
       col_3 = c(1, 2, 3, 4))
table_two <- c("b", "d")

When you set it up that way, something like this should work:

library(tidyverse)
table_one %>% filter(col_1 %in% table_two,
                     col_2 %in% table_two)

Answer 2

Here is a base R solution:

rawData1 <- "first second distance
 sample1    sample2    405
 sample3    sample4    400
 sample5    sample6    1
 sample7    sample8    20
 sample1    sample3    40"

rawData2 <- "sample
 sample1
 sample2
 sample8"

a <- read.table(textConnection(rawData1),stringsAsFactors=FALSE,header=TRUE)
b <- read.table(textConnection(rawData2),stringsAsFactors=FALSE,header=TRUE)

a[a$first %in% b$sample & a$second %in% b$sample, ]

...and the output:

> a[a$first %in% b$sample & a$second %in% b$sample, ]
    first  second distance
1 sample1 sample2      405

Answer 3

The best option could be inner_join twice, both with 1st column and 2nd column and then perform intersect of two result set.

library(dplyr)

df1 <- read.table(text = "Samp1 Samp2  Val
sample1    sample2    405
sample3    sample4    400
sample5    sample6    1
sample7    sample8    20
sample1    sample3    40", header = TRUE, stringsAsFactors = FALSE)
> df1
    Samp1   Samp2 Val
1 sample1 sample2 405
2 sample3 sample4 400
3 sample5 sample6   1
4 sample7 sample8  20
5 sample1 sample3  40

df2 <- data.frame(Samp = c("sample1",
                           "sample2",
                           "sample8"), stringsAsFactors = FALSE)
> df2
     Samp
1 sample1
2 sample2
3 sample8

#use inner_join between Samp1 with Samp and then again Samp2 with Samp
intersect(inner_join(df1,df2, by = c("Samp1" = "Samp")),
      inner_join(df1,df2, by = c("Samp2" = "Samp")))

The result will be:
    Samp1   Samp2 Val
1 sample1 sample2 405