Can I follow-up with what I've learned about my own myopia regarding sapply()?
First, I appreciate all the feedback. After thinking about it for a while I realized R designers have often chosen to accommodate interactive usage, and in that context, sapply() returning different types makes perfect sense. If applying both 'mean' and 'var' to multiple data sets in a list, it makes sense to return a matrix, but if applying just 'mean' the same list of data sets it makes sense to return a list, not a 1xN matrix. This works well in an interactive context but when writing robust applications, it is essential that routines return consistent types, especially if the parameters are determined from unpredictable user input. The behavior of functions like sapply() in R seems extraordinary compared to languages I am more familiar with like C, Java, or Python. In my case I was using sapply() to extract alignments from multiple BAM files that overlap exons of a gene. My application of sapply() returned a matrix with data sets across columns and exons down the rows. This worked well for most genes, but failed when run on a gene with only a single exon because sapply() returned a list instead of a matrix. This bug in my code was just waiting for the right set of inputs to trigger it. [ Some suggested using vapply() but don't think that would help in this case because the length of the return value from the applied function is variable and depends on how many exons are in the gene. Or perhaps I just don't understand vapply well. ] sapply() is behaving very similarly to the way the '[' and '[[' operators treat data frames. The extract operator '[' returns a vector when extracting a single column from a data frame, otherwise it returns a data frame. However both '[' and '[[' take a 'drop' parameter to control this behavior so you can get a consistent type back if you need it. I wish sapply() had a similar option. -csw ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
