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.

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

Munged sample sizes not equal to input #55

Open
rrydbirk opened this issue Jun 8, 2020 · 0 comments
Open

Munged sample sizes not equal to input #55

rrydbirk opened this issue Jun 8, 2020 · 0 comments

Comments

@rrydbirk
Copy link

rrydbirk commented Jun 8, 2020

For munging, I ran this:
python ldsc/mtag_munge.py
--sumstats Nalls2019/nallsEtAl2019_clean.tsv
--a1 A1
--a2 A2
--merge-alleles data/ldsc/w_hm3.snplist
--keep-pval
--p p
--out Nalls2019/Nalls2019

Following munging, I get "weird" N (sample sizes). As an example, SNP rs6678176 has N "378755.399715", but my input summary statistics file looks like this before munging (from nallsEtAl2019_clean.tsv):

SNP A1 A2 freq b se p N_cases N_controls N_total
rs6678176 T C 0.290 0.0322 0.0245 0.188 26421 442271 468692

I'm curious why these Ns are so different. Is this something I should worry about?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant