That can be a tough error to debug. It generally means you're attempting to access a function like a vector or data frame (using the []), but in your case, I wonder if it's not related to the previous data loading issue.
R doesn't seem to like the expression: raw_fusion$Sample ID. First, what is stored in Sample ID? Make sure that's what you expect. Then you might make sure raw_fusion$Sample ID is extracting the column you intend.
Can you create a small version of this code the reproduces the error, with the data included, with possibly just a few 'dummy' rows of data since I know it's proprietary? This is the reprex mentioned earlier. Otherwise it will be difficult to help you debug this.