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LiftOver for summary statistics #34
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Commits on Jul 15, 2023
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Liftover functionality for summary statistics
Functions are included under `mungesumstats.jl`. Consists of two user facing functions: `readchain` to read a chain file for liftover, and `liftover_sumstats!` to liftover a munged summary statistics DataFrame. To do includes handling the edge case where the target strand in the chain file has a negative strand and adding examples into the documentation.
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Commits on Jul 17, 2023
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Rename and edit liftover functions, documentation
`liftover_gwas!` is now `liftover_sumstats` to be in line with `mungesumstats!`. Additionally, `liftover_gwas!` can now be applied to AbstractVector{<:AbstractDataFrame}, in line with `mungesumstats` behavior. `parsechain` drops the "chr" prefix to be in line with `mungesumstats!` behavior. Function parameter `echain` renamed to `chain` (originally named `echain` for "expanded chain", but was needlessly verbose since we never use the output from `parsechain`). Documentation for the liftover functions added to the end of the summary statistics tutorial and mentioned in the GENCODE GTF parsing tutorial. Tests updated to test liftover functionality over a vector.
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Rename
liftover_sumstats!
toliftoversumstats!
All the other functions omit underscores; rename to match style.
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Commits on Jul 19, 2023
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Faster rewrite of findnewcoords (liftoversumstats!)
Rewrote `findnewcoords` to sort and then iterate through the summary statistics in order to liftover more efficiently. `readchain` also sorts the chain file now for that same purpose. This replaces the slower old code which used DataFrames.subset to find matching regions between builds. Also, added a bug fix to `readchain` where the ending coordinate was included: the chain format uses half-open intervals.
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Commits on Jul 31, 2023
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Commits on Aug 15, 2023
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Commits on Aug 17, 2023
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Commits on Aug 18, 2023
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Move liftover code to separate file
Moved liftover code from mungesumstats.jl to liftover.jl. Added some more error catching code (mainly for when lifted over indels no longer match the reference).
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Commits on Aug 20, 2023
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Commits on Aug 30, 2023
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