Adding anndata concatenation with bioalpha to main TileDB branch#116
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ariannalandini wants to merge 11 commits intotiledb_locusbreakerfrom
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Adding anndata concatenation with bioalpha to main TileDB branch#116ariannalandini wants to merge 11 commits intotiledb_locusbreakerfrom
ariannalandini wants to merge 11 commits intotiledb_locusbreakerfrom
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…id having actual 0 values rather than sparse
… using branch (#111) * Adding modification to run on scQTLs on Sanger * Add OT script (#109) * Add Credible Set Expansion feature to Fine-Mapping (#99) * Removing susie.cs.ht() because it should be taken directly from the flanders R package * Have customizable post susie QC parameters * Nevermind - function copied and pasted from gitlab, temporary solution until merge with github flanders r repo * Back to sourcing function rather than calling it from flanders R package (temporary solution) and fixing parameters * Forgot to remove susie_qc_cs_lbf_thr parameter from here * Added susie QC parameters to the nextflow schema * Rearraning post susie QC, so that loci disappearing becuase of QC are re-finemmaped with L=1. And overall L=1 loci do not go thorugh QC * Adding locusbreaker * Adding locus size parameter * Add report collecting loci that were re-finemapped with L=1 after being wiped out by post susie QC * Wrapped all code to go from susie output to rds list of dataframes object in a function * Adding credible set expansion and using function from susie output to rds format * Remove some parameters from list of those mandatory - if not specified, default is fine * Do not hardcode L=10, but rather use the assigned variable * Ok nevermind, reverting previous commit and adding also post susie QC parameters to required list * Removing hardcoding of L=10 for easier maintenance * Forgot to close parenthesis * Temporarely copy and paste functions from gitlab R package version * Computing also cs logsum - and adding it to the anndata obs * Fixed unmatching parenthesis * tile_lb_input parameters defined but not used. Assigning correct filename to tiledb_bfile parameter in test * Removing tuple since it's only one element * Revert "Merge branch 'tiledb_locusbreaker' into cs_expansion" This reverts commit fc15e3b, reversing changes made to 2059698. --------- Co-authored-by: arianna.landini <arianna.landini@external.fht.org> Co-authored-by: bruno-ariano <bruno.ariano.87@gmail.com> * Fixing KL for smaller loci (N SNPs < L) and identifying HLA region for GRCh 37 (#106) * Having HLA coordinates also in GRCh 37 * Checking for KL length in loci with less than L SNPs * When expanding credible sets, variance of lABFs not only must be different from 0, but also not NA (this happens with a single SNP in the locus) * Correct parameter (coloc_h5ad_input) for coloc input in example * adding script for creating anndata from OT --------- Co-authored-by: Arianna Landini <43240476+ariannalandini@users.noreply.github.com> Co-authored-by: arianna.landini <arianna.landini@external.fht.org> --------- Co-authored-by: bruno.ariano <bruno.ariano.87@gmail.com> Co-authored-by: arianna.landini <arianna.landini@external.fht.org>
…data concatenation * attach tdbsumstat to flanders * Remove patch to replace the chr string in SNP * Exclude from cs expansion loci of only one SNP - no variance --------- Co-authored-by: Arianna Landini <al37@sanger.ac.uk>
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In the spirit of tidying up branches, here the merge between the "main" TileDB branch and the one introducing bioalpha for concatenating annDatas - plus few small improvments.
@bruno-ariano can you please have a look? Especially that all TileDB locus breaker parameters are the most updated ones. Thanks!