**70**wrote:

New to R.

Problem: I have created objects `a`

and `b`

, a contains 1,200,000 rows and `b`

contains 5000 rows. I want to repeatedly sample 1000 rows from `a`

and compare the items in `a`

to those items in `b`

to find out how many overlapping items exist.

All I know is how to create an object:

```
a <- c(1,2,3,....L)
b <- c(1,2,3,....L)
```

...and, randomly sample `a`

:

```
c <- sample(a, 1000)
```

However, I don't know how to compare `a`

and `b`

to determine the number of overlapping items. My attempt at this with a simple if, then statement returned an error:

```
if (c==b) "TRUE" else "FALSE"
[1] "FALSE"
Warning messages:
1: In c == b :
longer object length is not a multiple of shorter object length
2: In if (c == b) "TRUE" else "FALSE" :
the condition has length > 1 and only the first element will be used
```

First problem, I need to know how to identify overlapping items between objects. Secondly, I need to repeat this multiple times (~10,000), perhaps through a for() loop?

Any insight will be much appreciated.

Are

`a`

and`b`

just numbers or are they genomic positions (e.g. from a`GRanges`

object)? The former case is quite simple:The latter case will depend on the object, though many objects allow intersects and comparisons. BTW, avoid

`for`

loops in R, they're really slow.97k