AshleyLab risk_scores issues

AshleyLab / risk_scores

LD Pred risk scores for afib

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Do you have to use different phenotype data in step3 of ldpred to logistic regression?

#20 jackosullivanoxford opened 4 years ago
1
Determining time of follow-up visit in UKBB data

#19 jackosullivanoxford opened 4 years ago
2
Results of sensitivity analysis when including TIA as event outcome

#18 jackosullivanoxford opened 4 years ago
2
What to do above the PRS outliers?

#17 jackosullivanoxford closed 4 years ago
1
Phenotype data from UKBB

#16 jackosullivanoxford opened 5 years ago
3
Validation data

#15 jackosullivanoxford opened 5 years ago
2
Compare the effect allele of GWAS SS and UKBB AFib Plink files

#14 jackosullivanoxford opened 5 years ago
0
Run all the steps using Cardioembolic GWAS Summary statistics

#13 jackosullivanoxford closed 4 years ago
3
Run analyses for all fractions of causation

#12 jackosullivanoxford closed 5 years ago
1
Make detailed methods/protocol

#11 jackosullivanoxford opened 5 years ago
0
Still need to add the other thromboembolic outcomes (e.g. PE, Arterial embolism and thrombosis: ICD code I74) to phenotype file

#10 jackosullivanoxford closed 5 years ago
1
If the PRS deciles still put the highest prevalence of ischemic stroke in the lowest decile group - check the following

#9 jackosullivanoxford opened 5 years ago
14
Test PRS on non-AFib patients with phenotype of ischemic stroke or no ischemic stroke

#8 jackosullivanoxford opened 5 years ago
0
Important covariates to include in logistic regression

#7 jackosullivanoxford opened 5 years ago
3
Make definitive files of a) total number of patients that have Afib in UKBB b) European patients with AFib in UKBB c) European patients with AFib with first degree relatives removed

#6 jackosullivanoxford opened 5 years ago
1
Steps to create kinship coefficient file and, ultimately, remove first degree relatives

#5 jackosullivanoxford opened 5 years ago
1
Quality control of Base and Target Data

#4 jackosullivanoxford opened 5 years ago
11
How does step 2 of LDpred measure the LD between the GWAS SS and the reference data?

#3 jackosullivanoxford closed 5 years ago
1
Check that GWAS summary statistics are mean centered and standardized to 1 (LDpred assumes this)

#2 jackosullivanoxford opened 5 years ago
1
Why is Step 1 of LDpred (--coord) not reading in the GWAS SS tsv file?

#1 jackosullivanoxford closed 5 years ago
1