Load a .rda file and iterate over its objects

Question

I loaded a rda file which basically its a list of dataframes. How do I iterate over is objects?

>load(data)
>attach(data)
 The following objects are masked _by_ .GlobalEnv:

GSE109597, GSE18897, GSE32575, GSE53232, GSE55205, GSE69039,
GSE83223, GSE87493, GSE98895
> R » objects()
[1] "GSE109597" "GSE18897"  "GSE32575"  "GSE53232"  "GSE55205"  "GSE69039" 
[7] "GSE83223"  "GSE87493"  "GSE98895"

Is `data` the path to the rda file? The `load()` command will return a vector with the names of all the objects loaded. You can use `mget()` to get a list of all those objects: `objs <- load(data); myobjs <- mget(objs)`. I would discourage you from using `attach()`. It's not a very good practice and it looks like you may have already done it a few times without properly calling `detach()` hence the warning message. — MrFlick, Apr 11 '19 at 19:35

r2evans · Accepted Answer · 2019-04-11T19:56:02.853

Two thoughts:

Load explicitly into a new empty environment, then work on them there:

e <- new.env(parent = emptyenv())
load(filename, envir = e)
out <- eapply(e, function(x) {
  # do something with x
})

From ?load, it returns a "character vector of the names of objects created, invisibly". If you capture the (invisible) vector, you should be able to do something like:

nms <- load(data)
for (nm in nms) {
  x <- get(nm)
  # do something with x
  # optional, save it back with assign(nm, x)
}
# or to capture all data into a list (similar to bullet 1 above)
out <- lapply(lapply(nms, get), function(x) {
  # do something with x
})

I prefer the first (environment-based) solution for a few reasons:

it will never overwrite anything in .GlobalEnv ... having learned that the hard way some times with unreproducible issues, this is huge for me
it encourages a list-like way of doing things, more important when most or all of the objects in the .rda file are the same "thing" (e.g., frame, list) and I plan on doing the same actions to each of them
if there is ever any doubt as to the source of the data, it won't clutter any of my namespace or global environment

Load a .rda file and iterate over its objects

1 Answers1