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Why FOCUS does not output TWAS p values? #29

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liqingbioinfo opened this issue Aug 20, 2024 · 0 comments
Open

Why FOCUS does not output TWAS p values? #29

liqingbioinfo opened this issue Aug 20, 2024 · 0 comments

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@liqingbioinfo
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Dear authors

   I ran through the Focus using code and data indicated on https://github.com/mancusolab/ma-focus/wiki/FOCUS:-Fine-mapping-TWAS-associations-in-a-single-ancestry-group. The output file contains the following header line, which does not contains TWAS pvalues. Can you please let me know if I missed something to generate them? Could I use twas_z_pop1 to derive TWAS P values?

focus finemap ./EA_WBC.Chen.2020/EA_WBC_new_munged_chr22.tsv.gz ./1000GP3_multiPop_allelesAligned/EUR/1000G.EUR.QC.allelesAligned.22 ./ea_fusion_genoa.db --chr 22 --locations 38:EUR --out ./focus_result

The header of my ouptut file:
block ens_gene_id ens_tx_id mol_name tissue ref_name type chrom tx_start tx_stop block_genes trait inference_pop1 inter_z_pop1 cv.R2_pop1 cv.R2.pval_pop1 ldregion_pop1 twas_z_pop1 pips_pop1 in_cred_set_pop1

Thank you
Qing

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