Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: filter_low_counts.R #2

Closed
kopardev opened this issue Oct 4, 2023 · 1 comment · Fixed by #10
Closed

feat: filter_low_counts.R #2

kopardev opened this issue Oct 4, 2023 · 1 comment · Fixed by #10
Assignees
@kopardev @kelly-sovacool
Labels
reneeTools RepoName
Milestone
2023w51_1222

Comments

@kopardev
Copy link
Member

kopardev commented Oct 4, 2023 •
edited by kelly-sovacool
Loading

input:
DEG_ALL/RSEM.genes.expected_count.all_samples.txt

output:
filtered data frame

function should:

  • remove genes with below threshold genes..threshold set by read count per samples + number of samples satisfying the min-read-count criteria
  • similar to min-read-counts filter ... but use CPM instead of read-count.
@kopardev kopardev added the reneeTools RepoName label Oct 4, 2023
@kopardev kopardev changed the title feat: function to remove genes with zeros across the board feat: "filter_low_counts.R" Oct 4, 2023
@kopardev kopardev changed the title feat: "filter_low_counts.R" feat: filter_low_counts.R Oct 4, 2023
@kopardev kopardev added this to the 2023w41_1013 milestone Oct 9, 2023
@kelly-sovacool
Copy link
Member

separate functions for count vs cpm.

@kopardev kopardev modified the milestones: 2023w41_1013, 2023w43_1027 Oct 23, 2023
kelly-sovacool added a commit that referenced this issue Dec 22, 2023
@kelly-sovacool
feat: implement filter_low_counts()
245a819 
resolves #2
@kelly-sovacool kelly-sovacool mentioned this issue Dec 22, 2023
Merged
5 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@kopardev kopardev

@kelly-sovacool kelly-sovacool

Labels
reneeTools RepoName
Projects
None yet
Milestone
2023w51_1222
Development

Successfully merging a pull request may close this issue.

Create filter_low_counts() CCBR/reneeTools
2 participants
@kopardev @kelly-sovacool