Has anyone tried using the `combinations`

argument in `hashedDrops`

? Unfortunately, I cannot fully understand the explanation in the help docs:(

Thanks in advance!

MIkhael

Input format for `combinations` in `hashedDrops`

0

Entering edit mode

Has anyone tried using the `combinations`

argument in `hashedDrops`

? Unfortunately, I cannot fully understand the explanation in the help docs:(

Thanks in advance!

MIkhael

1

Entering edit mode

Let's have a look at what `?DropletUtils`

says:

An integer matrix specifying valid _combinations_ of HTOs. Each row corresponds to a single sample and specifies the indices of rows in ‘x’ corresponding to the HTOs used to label that sample.

So let's say we have a matrix like:

```
x <- matrix(rpois(1000, 10), ncol=100) # made up
rownames(x) <- LETTERS[1:10]
x[,1:5]
## [,1] [,2] [,3] [,4] [,5]
## A 9 9 16 8 9
## B 12 15 7 12 9
## C 10 7 14 13 16
## D 13 5 13 7 5
## E 8 7 13 10 6
## F 10 10 12 7 7
## G 12 15 9 6 8
## H 9 13 12 11 11
## I 5 10 11 6 4
## J 9 7 12 11 6
```

I might then have this `combinations`

:

```
combinations <- rbind(
Sample1 = c(1, 5), # Sample 1 is marked by A and E
Sample2 = c(1, 4), # Sample 2 is marked by A and D
Sample3 = c(2, 3) # Sample 3 is marked by B and C
)
```

and so on. This particular example uses combinations of 2, but you could also imagine higher-order combinations if your experimental design was more ambitious. I do recall there being some constraints though - something like the number of HTOs used in each sample must be less than half the total number of HTOs.

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