Make it easier to append annotations to an FCS file; align getFcsFile, getFcsFiles and annotateFcsFile

[zbjornson]

The docs for annotateFcsFile rightly warn that using it will overwrite existing annotations and say to use getFcsFile first. However, getFcsFile[s] returns a list and annotateFcsFile expects a list, so this is tedious to do.

Current method:

fa = data.frame(file$annotations)
annoList = as.list(with(fa, setNames(value, name)))
annoList[["New Anno"]] <- "abcd"

[zbjornson]

#47 didn't actually address this, and I'm not sure it should have been merged as it was meant to be a convenience function that papers over the list of lists that our API uses. We still need a doc example that shows taking an FCS file (from getFcsFile and getFcsFiles) and appending new annotations to it.

Current method I'm using:

files = getFcsFiles(...)
file = files[[1,]]
annos = file$annotations[[1]]
annos[nrows(annos+1,] <- list(name="abc", value="def")

[gegnew]

Is line 2 there supposed to be file = files[1,]? The double-bracket notation throws an error