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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Update the reference of addMotifAnnotations #1952

Closed Gavin-Lijy closed 1 year ago

Gavin-Lijy commented 1 year ago

I noticed you have replaced variable "name" with "annoName", could you please update it in function reference for the sake of usage?

addMotifAnnotations <- function(
  ArchRProj = NULL,
  motifSet = "cisbp",
  annoName = "Motif",
  species = NULL,
  collection = "CORE",
  motifPWMs = NULL,
  cutOff = 5e-05, 
  width = 7,
  version = 2,
  force = FALSE,
  logFile = createLogFile("addMotifAnnotations"),
rcorces commented 1 year ago

Hi @Gavin-Lijy! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, how will we be able to help? Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

rcorces commented 1 year ago

will happen with the next release. The best place to find this information is via ? in R