-
Notifications
You must be signed in to change notification settings - Fork 9
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
feat: extract credible sets and studies from eQTL Catalogue finemapping results #514
Conversation
…FromSource` nullable
… into il-eqtl-susie
… into il-eqtl-susie
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Wonderful!
StructField("sample_group", StringType(), True), | ||
StructField("tissue_id", StringType(), True), | ||
StructField("tissue_label", StringType(), True), | ||
StructField("condition_label", StringType(), True), |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
to be added to the study index
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yakov mentioned that carrying it over in the study index should be enough.
This PR includes:
credible_set
andstudy_index
datasets based on the eQTL Catalogue finemapping results for all eQTLs that significantly influences gene expression.Metrics
Note
This PR only processes results where the quantification method is ge.
Based on a discussion with @DSuveges and @d0choa, we will bring credible sets from all methods. I suggest that these changes happen in a subsequent PR, to checkpoint the work achieved here in case we want to revert.
coauthored with @d0choa