SinomeM/QCtreeCNV

Issues

• add merge CNVRs to the fast implementation?

  #17 opened 2 years ago by SinomeM
  0

• `cnvr_fast()` need to make it optional to check for the possibility of just one cluster

  #21 opened 2 years ago by SinomeM
  0

• `check_inputs()` is defined but not integrated in `qc_pre()`

  #20 opened 2 years ago by SinomeM
  0

• Check better the behaviour of qctree()

  #19 opened 3 years ago by SinomeM
  0

• Fix qctree_pre()

  #18 opened 3 years ago by SinomeM
  0

• add the possibility to skip individual steps in `qctree()`

  #6 opened 3 years ago by SinomeM
  0

• check when `dt` copies are made and if it is really necessary

  #15 opened 3 years ago by SinomeM
  0

• All functions needs some initial check to be sure the inputs are correct

  #5 opened 3 years ago by SinomeM
  2

• ADD a function that run the entire pipeline w/ all required checks

  #7 opened 3 years ago by SinomeM
  2

• try vectorize some for loops

  #8 opened 3 years ago by SinomeM
  1

• split qc_tree() into two funtions, one to just check the inputs (+ preprocessing) the other to run the pipelne ?

  #12 opened 3 years ago by SinomeM
  1

• select_filter() should create the length column if not already present

  #13 opened 3 years ago by SinomeM
  0

• numsnp column is necessary in select_stitch() funciton but it is not listed in the documentation

  #11 opened 3 years ago by SinomeM
  1

• Write some minimal formal documentation for each exported function + the package itself

  #14 opened 3 years ago by SinomeM
  0

• add support for the use of snppos file in `extractRDS()`

  #4 opened 3 years ago by SinomeM
  2

• integrate TABIX

  #10 opened 3 years ago by SinomeM
  1

• compute CNVRs per locus separately?

  #2 opened 3 years ago by SinomeM
  1

• add the possibility to parallelize the slower steps

  #9 opened 3 years ago by SinomeM
  1

• Integrate CNVgears functions

  #1 opened 3 years ago by SinomeM
  1

• Integrate initail QC and stitching as a function in the package

  #3 opened 3 years ago by SinomeM
  1