cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium

Home Page:https://cumc.github.io/xqtl-protocol/

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Wishlist for susie finemapping piepline

SamuelSun2000 opened this issue · comments

We plan to:

  1. Unify interface for mvsusie
  2. Robustness against mismatch of covar and phenotype, with regid specification
  3. Minimize the need of pre-processing to get 2
  • 1. In [uni_susie_1], make the pipeline can accept format of a list, each row containing a single cell data & the file address and fixed some bugs.
  • 2. Subset the recipe 1071674498171_ pic and make it into phenotype list and covariate list in the command generator section. Process the covariate files Then the input list for [uni_susie_1] should be ready.

Workflow Optimization

  • 3. Isolate step [uni_susie_2] from step 1. Then, that function can be used as reading lists of susie objects.
  • 4. maybe In [uni_susie_1], unwrap the list fitted so that the result can be easier to handle, instead of a list of susie objects.