Hi everyone

Probably, my question fits better in any global R blog, but I am not sure. Anyway, this is que question:

I have applied synergise function to a set of MSe/HDMSe files and then saved the result as .rda file:

syn <- synergise(.....)

save(syn, file = ......)

Now, I would like to load again that data to follow with the synapter pipeline. To this, I have tried with:

syn <- load(filename)

and when I started to convert it into MSnbase object, (x <- as(syn, "MSnSet")), I get the following message:

Error in as(syn, "MSnSet") :
  no method or default for coercing “character” to “MSnSet”

Applying class function to syn, class(syn), returns [1] "character"

How can I save my data after synergise function and then load it again?

Thanks in advance

Samuel

load will load the object from your file in your global environment - there is no need for assignment.

> x <- 1:10
> save(x, file = "x.rda")
> rm(x)
> load("x.rda")
> ls()
[1] "x"
> x
 [1]  1  2  3  4  5  6  7  8  9 10

If you assign the output, you will get the name of the variable, instead of its content.

> x <- load("x.rda")
> x
[1] "x"

See saveRDS and readRDS for your use case.

> xx <- 1:10
> saveRDS(xx, file = "xx.rds")
> rm(xx)
> zz <- readRDS("xx.rds")
> zz
 [1]  1  2  3  4  5  6  7  8  9 10

There are several ways to save and load an R object. You could use 'save' and 'load' as you tried. 'load' will add the object to your global environment (and return the object name invisible). That's why your loading fails. You overwrite the real object by its name. Try just: 'load("yourfile")' instead of 'syn <-load("yourfile")'. Another way of saving/reading R objects would be 'saveRDS' and 'readRDS'. While 'save'/'load' could save/load multiple objects 'saveRDS'/'readRDS' could handle only a single object. Please have a look at the corresponding manual pages.