v2 release #135
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v2 release #135
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…hich can vary in size). [TODO: ensure PCA is done on reference dataset]
* fix action * Label sampleset on PCA plots in report.qmd * add reference panel name * Plot distributions for multiple adjustment methods * fix action o_O * Small edits for clarity/simplicity * More informative legends for PCA plots * Move pointer to online documentation closer to the header. * Add in match_flipped (Matches strand flip) to variant log table (was previously missing) * Oops * Oops (v2 double set of quotes) * Add reference intersection statistics to report (#129) * count intersection hit/miss * add count to report * Ancestry version of the report needs to indicate variants that were excluded because they do not match the reference ToDo: replace values to be in comparison of % of variants in target that are in reference * fix intersect stats * hide ancestry headers automatically * fraposa dev -> fraposa v0.1.0 * fix container tags * melt non-ancestry aggregated scores * update conda requirements * upgrade quarto to fix error * fix dockerfile * empty commit to trigger action with fresh cache --------- Co-authored-by: Benjamin Wingfield <[email protected]>
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Aug 1, 2023
* update conda module definitions * update pgscatalog_utils container reference * fix container reference * fix conda package names * add missing packages
…nly increase MAF to 5%, and decrease leniency of HWE).
Improve variant selection for PCA
* add --error-on-freq-calc to improve scoring efficiency * only enable no-mean-imputation when ancestry doesn't run * test plink log matches scorefile n lines
* add plink2 explanation * docs review * be clear about --max_cpus and --max_memory * Update README.md * minor fixes * ancestry how-to * update docs * make downloading clearer * Edit TOC, plink2, and name of ancestry doc * Edit plink2 + link * Edit results dirs * Add motivation (test figure caption insertion) * Try to fix figure caption * Try to fix figure caption 2 * Add new figure with ancestry adjustment methods (using the new labels) * Change size of figures * Test citations * Change citations to numbered footnotes * Add more explanation * Edits to previous sections * Scaffold implementation * More implementation details * More implementation details * List formatting (very tedious spacing requirements) * List formatting (very tedious spacing requirements) v2 * ToDo: add back interpretation section (e.g. example analysis in UKB) * Update README.md * Update index.rst * Edits * Citation edits * Edits to report/output page * Edit to html description * Added extra column descriptions for the output tables (variant matching) * Additional edits * More doc edits * Edits from Mike * Citation edits * Add information about feedback & link to discussion board * Additional information re: PCA to reflect new defaults and future improvements * Bring nextflow_schema.json up to date with origin/dev * Update changelog.rst * Update geneticancestry.rst fix typo --------- Co-authored-by: smlmbrt <[email protected]>
smlmbrt
approved these changes
Aug 7, 2023
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