LiftOver for summary statistics #34
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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.
`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.
All the other functions omit underscores; rename to match style.
Codecov ReportPatch coverage:
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## master #34 +/- ##
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+ Coverage 60.38% 64.19% +3.81%
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Files 12 12
Lines 982 1472 +490
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+ Hits 593 945 +352
- Misses 389 527 +138
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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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Rewrote the code for liftover to replace the calls to DataFrame.subset when finding the matching region in the chain file. Processes 100,000+ variants a second now. |
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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Added code for normalizing GWAS to the reference build and renaming the SNPs with rsIDs from a VCF file. Also added to liftover functionality to liftover indels as well as SNPs. |
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Edits still needed:
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Performs liftover on munged summary statistics. Added in documentation and tests for the functions.
New functions: