search

FINNGEN / META_ANALYSIS

Tools for doing x way meta-analysis
MIT License
6 stars 14 forks source link

Leave-one-out analysis has missing fields #42

Closed juhaa closed 3 years ago

juhaa commented 3 years ago

For some variants, number of fields does not match the number of columns in a leave-one-out meta-analysis output. Example:

Ok variant:

CHR|POS|REF|ALT|SNP|FINNGEN_beta|FINNGEN_sebeta|FINNGEN_pval|FINNGEN_af_alt|FINNGEN_af_alt_cases|FINNGEN_af_alt_controls|FINNGEN_nearest_genes|UKBB_beta|UKBB_sebeta|UKBB_pval|ESTBB_beta|ESTBB_sebeta|ESTBB_pval|ESTBB_af_alt|ESTBB_AF.Cases|ESTBB_AF.Controls|ESTBB_b37_chr|ESTBB_b37_pos|ESTBB_b37_ref|ESTBB_b37_alt|ESTBB_liftover_info|ESTBB_af_gnomad|ESTBB_af_fc|all_meta_N|all_inv_var_meta_beta|all_inv_var_meta_sebeta|all_inv_var_meta_p|all_inv_var_het_p|leave_FINNGEN_N|leave_FINNGEN_inv_var_meta_beta|leave_FINNGEN_inv_var_meta_sebeta|leave_FINNGEN_inv_var_meta_p|leave_FINNGEN_inv_var_meta_het_p|leave_UKBB_N|leave_UKBB_inv_var_meta_beta|leave_UKBB_inv_var_meta_sebeta|leave_UKBB_inv_var_meta_p|leave_UKBB_inv_var_meta_het_p|leave_ESTBB_N|leave_ESTBB_inv_var_meta_beta|leave_ESTBB_inv_var_meta_sebeta|leave_ESTBB_inv_var_meta_p|leave_ESTBB_inv_var_meta_het_p

-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-| 1|108391|A|G|1:108391:A:G|7.17e-02|1.81e-01|6.92e-01|0.0019977|0.00213562|0.00198638|OR4F5|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|NA|1|7.17e-02|1.81e-01|6.92e-01|NA|0|NA|NA|NA|NA|1|7.17e-02|1.81e-01|6.92e-01|NA|1|7.17e-02|1.81e-01|6.92e-01|NA|

Not ok variant:

CHR|POS|REF|ALT|SNP|FINNGEN_beta|FINNGEN_sebeta|FINNGEN_pval|FINNGEN_af_alt|FINNGEN_af_alt_cases|FINNGEN_af_alt_controls|FINNGEN_nearest_genes|UKBB_beta|UKBB_sebeta|UKBB_pval|ESTBB_beta|ESTBB_sebeta|ESTBB_pval|ESTBB_af_alt|ESTBB_AF.Cases|ESTBB_AF.Controls|ESTBB_b37_chr|ESTBB_b37_pos|ESTBB_b37_ref|ESTBB_b37_alt|ESTBB_liftover_info|ESTBB_af_gnomad|ESTBB_af_fc|all_meta_N|all_inv_var_meta_beta|all_inv_var_meta_sebeta|all_inv_var_meta_p|all_inv_var_het_p|leave_FINNGEN_N|leave_FINNGEN_inv_var_meta_beta|leave_FINNGEN_inv_var_meta_sebeta|leave_FINNGEN_inv_var_meta_p|leave_FINNGEN_inv_var_meta_het_p|leave_UKBB_N|leave_UKBB_inv_var_meta_beta|leave_UKBB_inv_var_meta_sebeta|leave_UKBB_inv_var_meta_p|leave_UKBB_inv_var_meta_het_p|leave_ESTBB_N|leave_ESTBB_inv_var_meta_beta|leave_ESTBB_inv_var_meta_sebeta|leave_ESTBB_inv_var_meta_p|leave_ESTBB_inv_var_meta_het_p

-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-| 1|97269|T|TAC|1:97269:T:TAC|NA|NA|NA|NA|NA|NA|NA|-6.39e-03|2.46e-02|7.95e-01|5.46e-02|6.37e-02|3.91e-01|0.134664490818977|0.138677342719711|0.134625304677773|2|243181793|T|TAC|.|0.e+00|NA|2|1.54e-03|2.3e-02|9.46e-01|3.72e-01|2|1|5.46e-02|6.37e-02|3.91e-01|NA|1|-6.39e-03|2.46e-02|7.95e-01|NA