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LiftOver for summary statistics #34

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Commits on Jul 15, 2023

  1. 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.
    danielduyvo committed Jul 15, 2023
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Commits on Jul 17, 2023

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  2. 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.
    danielduyvo committed Jul 17, 2023
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  3. Rename liftover_sumstats! to liftoversumstats!

    All the other functions omit underscores; rename to match style.
    danielduyvo committed Jul 17, 2023
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  4. Bug fix

    danielduyvo committed Jul 17, 2023
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Commits on Jul 19, 2023

  1. 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.
    danielduyvo committed Jul 19, 2023
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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

  1. Lifting over indels

    danielduyvo committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. 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).
    danielduyvo committed Aug 18, 2023
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Commits on Aug 20, 2023

  1. Harmonize variant names

    danielduyvo committed Aug 20, 2023
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Commits on Aug 30, 2023

  1. Change variable name

    danielduyvo committed Aug 30, 2023
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