search

bogdanlab / focus

FOCUS: Fine-mapping Of CaUsal gene Sets
GNU General Public License v3.0
44 stars 17 forks source link

P less than 5e-8 but it says doesnt' exist #30

Closed Captain-Pam closed 1 year ago

Captain-Pam commented 3 years ago

Hi Thank you for your tool. It is very helpful for us. But I have a question about it. 1) my GWAS had SNP CHR BP A1 A2 BETA SE P MAF,after munging the data P is not in the data, and result of fine map is empty, the log file says there is not p < 5e-8 ....

my munge code

focus munge $GWAS --N 80610 --N-cas 20806 --snp SNP --a1 A1 --a2 A2 --p P --frq MAF --output $CLEAN_OUT/AAA_combind_clean the result was going to get a lot fewer rows.(did i do something wrong?) what is the munging data main function?

my fine map code

focus finemap $CLEAN_OUT $REF $PREDICT_DB --chr 9 --tissue Brain_Caudate_basal_ganglia --plot --output $FINE_OUT/AAA_combind_clean_fine_chr9 2) only analyze one chromosome at a time?Or an tissue?The inability to compare genes in multiple tissues simultaneously?Like 13 GTEX brain tissues

Thank you ! look forward to your reply! Have a nice day!

sookwah-yee commented 2 years ago

Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?

Captain-Pam commented 2 years ago

Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?

There has been no solution to this problem. If you are interested, can we try to solve it together?

sookwah-yee commented 2 years ago

I am interested to work together. I also have empty log file. I notice that the p<5e-8 is a warning and wasn't an error. I also tried using lower threshold and does not work. It is frustrating and I cannot move forward using it. I also email the creator, but has not heard back from him.

sookwah-yee commented 2 years ago

Hi @Captain-Pam, I think I may have a reason. I need to use the focus.db rather than gtex_v7.db https://www.dropbox.com/s/ep3dzlqnp7p8e5j/focus.db?dl=0 Try and see if it works for you after switching to focus.db. It is working for me now. I am not sure why gtex_v7.db not working for me.

quattro commented 2 years ago

Apologies for delayed response. Seeing this thread now. A few things:

  1. I plan to replace the v7 db with an updated v8 soon.
  2. Can you manually output regions that contain p < 5e-8 and contrast those with the pre-defined LD blocks from LDetect? It may be that some loci are dropped.
Captain-Pam commented 2 years ago

Hi @sookwah-yee @quattro. it is strange, seeing the example, it used the gtex_v7.db. However, I downed GTEx v8.db from PredictDB website (mashr model) to created the focus.db file by using ‘FOCUS import‘ command. So I agree with @quattro , maybe the locus is not in the LD block from LDetect.

sookwah-yee commented 2 years ago

Hi @Captain-Pam and @quattro, thank you for sharing the information for what you did.
I would like to try using GTEx v8.db soon and I wonder which one did you use @Captain-Pam ? There are four different one under Mashr model. Also if I use the v8.db and do the focus.import, do I need to convert the RSID to the different format? mashr_eqtl.tar: PrediXcan’s and S-PrediXcan’s support on expression mashr_sqtl.tar: PrediXcan’s and S-PrediXcan’s support on splicing gtex_v8_expression_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan expression’s LD reference gtex_v8_splicing_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan splicing’s LD reference