The results from F4-ratio and D-statistic are different
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 15/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start with the supplied topology and the qpF4ratio version 300 and qpDstat version 701 outputs. Compare the population ordering and the meaning of each statistic before assessing whether the results are actually contradictory. Done means providing a supported interpretation or identifying a reproducible defect.
Written by the indexing model from the issue text.
Description
Dear @bumblenick
I have a few questions about the results from F4-ratio (qpF4ratio) and D-statistic (qpDstat). Can I detect introgression between two populations using F4-ratio on a genome-wide scale? I ran these two methods for a same dataset, as a result, the qpF4ratio detected EUR has about 1.1% introgression from IBEX1, but the qpDstat told me the IBEX1 share more derived allele with AFR. the topology among these five populations is following,
results from qpF4ratio version: 300
result: BEZ2 Outgroup EUR IBEX1 : BEZ2 Outgroup AFR IBEX1 0.988603 0.000951 1039.104
result: BEZ2 Outgroup AFR IBEX1 : BEZ2 Outgroup EUR IBEX1 1.011527 0.000973 1039.104
results from qpDstat version: 701
result: Outgroup IBEX1 EUR AFR 0.0045 0.001616 2.816 39371 39014 5123960
Can you help interpret this contradict results, many thanks!
Best Wishes
zhuqing
- Dominant language
- C
- Stars
- 236
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
Getting set up
This project ships no dev container, Dockerfile or contributing guide, so setting up is up to you: start from its README, and see our first-contribution guide for the general steps.
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from DReichLab/AdmixTools
-
Difficulty 5/5 Over a week Newbie friendliness 35/100
DReichLab/AdmixTools#125 · 7 comments ·
-
Difficulty 4/5 3-5 days Newbie friendliness 25/100
DReichLab/AdmixTools#123 · 2 comments ·
-
Difficulty 5/5 Over a week Newbie friendliness 20/100
DReichLab/AdmixTools#122 · 2 comments ·
-
Difficulty 4/5 3-5 days Newbie friendliness 25/100
DReichLab/AdmixTools#121 · 1 comment ·
-
Difficulty 4/5 3-5 days Newbie friendliness 25/100
DReichLab/AdmixTools#117 · 3 comments ·
All issues in DReichLab/AdmixTools
Similar issues
-
severity: low
Difficulty 2/5 1-3 hours Newbie friendliness 70/100
luainkernel/lunatik#1853 ·
Maintainers usually reply within 1 day
-
Difficulty 2/5 Half a day Newbie friendliness 70/100
Maintainers usually reply within 1 day
-
Difficulty 2/5 1-3 hours Newbie friendliness 66/100
Maintainers usually reply within 5 days
-
constants.h: M_PI / M_PI_2 fallbacks cause -Wambiguous-macro when H3 is compiled as a Clang moduleOpen
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
Maintainers usually reply within 1 day
-
area:backend bug launch:p2 scope:core
Difficulty 2/5 1-3 hours Newbie friendliness 62/100
Chelis-Lang/chelis#3494 ·
Maintainers usually reply within 1 day