lifebit-ai gwas issues - Githubissues

lifebit-ai / gwas

GWAS pipeline using SAIGE

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switch_platekeys executed when testing flag not given

#83 mcamarad closed 3 years ago
1
Adds simulation of phenotypes

#82 mcamarad closed 3 years ago
0
Adds querying feature for CB output

#81 mcamarad closed 3 years ago
0
Fix discrepancies between handling testing CB data and real CB data within transform_cb_output.R script

#80 mcamarad closed 3 years ago
0
Fixes #76 #77 #78

#79 mcamarad closed 3 years ago
0
Fix error around length of resulting pheno columns

#78 mcamarad closed 4 years ago
0
Fix unexpected behaviour around columns full of NAs

#77 mcamarad closed 4 years ago
0
Adapting vars names to real CB output breaks CI tests

#76 mcamarad closed 4 years ago
0
Adds blacklist for continuous variables that users don't want to transform

#75 mcamarad opened 4 years ago
0
Updates pheno_data, pheno_metadata from CB export

#74 cgpu closed 3 years ago
0
Adds extensive testing and fixes from backlog

#73 mcamarad closed 4 years ago
1
Adds testing scenario for working with real pheno data and synthetic genotypes

#72 mcamarad closed 4 years ago
0
all_contrasts & case_vs_group_contrasts CI test fail due to memory issues

#71 mcamarad opened 4 years ago
0
Fix null behaviour on report when LDSC is not executed

#70 mcamarad closed 4 years ago
0
Add exception in continuous data transformations to not be computed on PCs

#69 mcamarad closed 4 years ago
0
Refactor to have only one process

#68 cgpu closed 4 years ago
0
Adds GWAS catalogue as input for genetic correlation

#67 mcamarad closed 4 years ago
1
ToDo: Investigate if the stats for this population can be custom

#66 cgpu opened 4 years ago
1
ToDo: Refactor to allow the user to provide ldsc/assets as a parameter

#65 cgpu closed 4 years ago
0
Allow user to input LD scores files for LDSC

#64 mcamarad closed 4 years ago
0
Improves handling of missing data

#63 mcamarad closed 4 years ago
1
Add dataframe format (.csv) for encoding mapping jsons

#62 mcamarad closed 4 years ago
0
Explore how to extract relevant results from LDSC output to integrate it in the report.

#61 mcamarad opened 4 years ago
0
Adds gh actions ci

#60 mcamarad closed 4 years ago
0
REVIEW DIFF ONLY - DON'T MERGE

#59 cgpu closed 4 years ago
0
Adds GWAS catalogue summary stats as LDSC input for genetic correlation

#58 mcamarad closed 4 years ago
0
Adds Genetic correlation and heritability analysis within the pipeline

#57 mcamarad closed 4 years ago
3
Replace awk command

#56 cgpu opened 4 years ago
0
Implement chrX, swap X with 23 for create_report process

#55 cgpu opened 4 years ago
0
Split gwas_filtering, step_2 SAIGE by autosomes, sex chromosomes (will only use X not Y)

#54 cgpu opened 4 years ago
0
Replace awk with gawk

#53 cgpu opened 4 years ago
0
Restore old behaviour to not use CB as input

#52 mcamarad opened 4 years ago
0
Check that n_cases is an integer in output matrix from SAIGE and also in the report

#51 mcamarad closed 4 years ago
1
Improve strategy to handle NA during and after processing of covariates & phenotypes

#50 mcamarad closed 4 years ago
0
Implement multiple contrast reporting and handling of results

#49 mcamarad opened 4 years ago
0
Implement querying instances and arrays functionality

#48 mcamarad closed 3 years ago
0
Opportunity to be more explicit: Use package::function() call

#47 cgpu opened 4 years ago
0
Expose awk query as param, see here:

#46 cgpu opened 4 years ago
0
Opportunity for refactor: Flatten nested if (if (case_group != 'None'){

#45 cgpu closed 4 years ago
0
Opportunity for refactor: flatten nested ifs

#44 cgpu closed 4 years ago
0
Add tests to cover all run scenaria.

#43 cgpu closed 4 years ago
0
Add process to analyse X chr

#42 cgpu opened 4 years ago
0
Implement str detection for mapping phenoCol to any variable/filename used in the scripts

#41 mcamarad opened 4 years ago
0
Implement continuous variable normalisation

#40 cgpu closed 3 years ago
0
Allow continuous variable as PHE

#39 cgpu closed 4 years ago
4
Integration of cohort browser output to GWAS pipeline #10122 #10296 #10294

#38 mcamarad closed 4 years ago
1
plinkTestCh is not used as input anywhere

#37 cgpu closed 4 years ago
1
qqman::manhattan(): CHR should be numeric, do you have X,Y,MT? If so change to numbers and try again

#36 cgpu opened 4 years ago
3
Implements extra filtering, adds dataviz report

#35 cgpu closed 4 years ago
0
Add validate inputs process

#34 cgpu opened 4 years ago
0

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