I notice that in the ballgown constructor there is an option to enter a "bamfiles" vector, as described in the ballgown manual here:

bamfiles                optional vector of file paths to read alignment files for each sample. If provided,

                               make sure to sort properly (e.g., in the same order as samples). Default NULL.

I don't understand what the use for this is though.  I do have bam files, but if I just leave this vector as NULL, am I losing some downstream capability?

Thanks!  

UPDATE:

I found the answer to my question in the ballgown github site, here:   https://github.com/alyssafrazee/ballgown

• "The bamfiles component isn't currently used by any ballgown functions, but it could come in handy for users of RSamtools or similar packages."

I found the answer to my question in the ballgown github site, here:   https://github.com/alyssafrazee/ballgown

• "The bamfiles component isn't currently used by any ballgown functions, but it could come in handy for users of RSamtools or similar packages."