CODEWITHSUNDEEP
rdata.tabledtplyr
zhang
zhang

Reputation: 543

How to filter a data.table based on an uncertain number of conditions?

Given the following data.table in R:

set.seed(123666)
dt <- data.table(sample1 = sample(10), 
                 sample2 = sample(10),
                 sample3 = sample(10),
                 sample4 = sample(10), 
                 sample5 = sample(10),
                 sample6 = sample(10))

dt
    sample1 sample2 sample3 sample4 sample5 sample6
 1:       2       6       3       9       1       2
 2:      10       9      10       3       7       5
 3:       6      10       8       5       5       1
 4:       8       2       9       8       6       6
 5:       5       4       5      10      10       8
 6:       7       1       7       4       4      10
 7:       4       3       1       6       3       7
 8:       1       5       6       1       2       3
 9:       3       7       2       2       8       9
10:       9       8       4       7       9       4

Let's assume the first 3 samples are in group_a and the last 3 samples are in group_b. Now we want to filter rows that satisfy the condition of having at least 2 out of 3 samples greater than 2 in each group. In the given case, we can achieve this using the following code:

group_a <- paste0('sample', seq(1,3))
group_b <- paste0('sample', seq(4,6))

dt[rowSums(dt[, ..group_a, with = FALSE] > 2) >= 2 & rowSums(dt[, ..group_b, with = FALSE] > 2) >= 2]

   sample1 sample2 sample3 sample4 sample5 sample6
1:      10       9      10       3       7       5
2:       6      10       8       5       5       1
3:       8       2       9       8       6       6
4:       5       4       5      10      10       8
5:       7       1       7       4       4      10
6:       4       3       1       6       3       7
7:       3       7       2       2       8       9
8:       9       8       4       7       9       4

Now, let's consider a data.table where each column still represents a sample name, but the number of samples is uncertain. There is an additional variable group describing the grouping of samples:

group <- paste0('sample', seq(1,6))
group_id <- c(rep('group_a', 3), rep('group_b', 3))
names(group) <- group_id 

group
  group_a   group_a   group_a   group_b   group_b   group_b 
"sample1" "sample2" "sample3" "sample4" "sample5" "sample6"

How to accomplish this task using the data.table syntax and with the most concise code possible?

Upvotes: 2

Views: 76

Answers (2)

langtang
langtang

Reputation: 24722

Here is an alternative that is not as slick as @Ritchie Sacramento's solution above, but might be of interest:

Make a long version of the data

long_dt = melt(dt[,id:=.I], "id")[data.table(variable = group, group=names(group)), on="variable"]

Make a helper function

f <- \(d,v,n) d[, sum(value>v),group][, sum(V1>=n)>=.N]

Use the helper function for any values v and n. For example to filter rows where each group has at least 2 values exceeding 4, you can do:

dt[long_dt[,f(.SD,4,2),id][V1==T,id]]

Output:

   sample1 sample2 sample3 sample4 sample5 sample6    id
     <int>   <int>   <int>   <int>   <int>   <int> <int>
1:      10       9      10       3       7       5     2
2:       6      10       8       5       5       1     3
3:       8       2       9       8       6       6     4
4:       5       4       5      10      10       8     5
5:       9       8       4       7       9       4    10

Upvotes: 1

lroha
lroha

Reputation: 34376

You can split on the names and iterate over the list to subset the columns and check your conditions then reduce the result to subset the rows:

library(data.table)

dt[Reduce(`&`, lapply(split(group, names(group)), \(x) rowSums(dt[, .SD, .SDcols = x] > 1) >= 2 )), ]

   sample1 sample2 sample3 sample4 sample5 sample6
 1:       2       6       3       9       1       2
 2:      10       9      10       3       7       5
 3:       6      10       8       5       5       1
 4:       8       2       9       8       6       6
 5:       5       4       5      10      10       8
 6:       7       1       7       4       4      10
 7:       4       3       1       6       3       7
 8:       1       5       6       1       2       3
 9:       3       7       2       2       8       9
10:       9       8       4       7       9       4

All rows meet your example criteria, but if we change it to at least two values greater than two, we can see that it works:

dt[Reduce(`&`, lapply(split(group, names(group)), \(x) rowSums(dt[, .SD, .SDcols = x] > 2) >= 2 )), ]

   sample1 sample2 sample3 sample4 sample5 sample6
1:      10       9      10       3       7       5
2:       6      10       8       5       5       1
3:       8       2       9       8       6       6
4:       5       4       5      10      10       8
5:       7       1       7       4       4      10
6:       4       3       1       6       3       7
7:       3       7       2       2       8       9
8:       9       8       4       7       9       4

@r2evans suggested an alternative that might offer better performance in the context of a large number of groups.

dt[rowSums(sapply(split(group, names(group)), \(x) rowSums(dt[, .SD, .SDcols = x] <= 2) >= 2 )) == 0, ]

Upvotes: 1

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