Issue fixes for data.frame check and file check

[maotian06]

Description

Fixed two bugs related to R version changes:

1. add a check for data.frame which is appended to the check for matrix.
2. change exists() function to file.exists() function.

Checklist

• [x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• [x] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• [x] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [ ] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
• [x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [ ] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

[tyamaguchi-ucla]

@maotian06 I made you an admin for this repo. You should be able to add branch protection rules.

[tyamaguchi-ucla]

@maotian06 Also, as you've changed multiple if blocks, if you haven't, this PR needs to be tested to confirm that no issues were introduced.

[jarbet]

Looks generally good to me. I've added one minor comment. Anything else to add @jarbet?

We should be good to go as long as the test cases work without any issues.

The PR LGTM. However, I cannot get the README examples to work on my Mac or cluster. It would be good for someone to confirm that these work.

When trying to run them on my Mac, it crashes.

I'm trying to get it to work on the cluster with the R module, but I need to install python. Maybe it would be good to create some instructions for how to successfully install iSubGen? @tyamaguchi-ucla - do the README examples work for you?