[trans] trans.map_permutations(): KeyError: 'r2'

[lintingyi2014]

The trans output doesn't seem to output these columns necessary for permutations. (https://github.com/broadinstitute/tensorqtl/blob/master/docs/outputs.md) I am using trans_df_appliedperm = trans.apply_permutations(trans_df_perm,trans_df) where trans_df is the dataframe after filtering_cis.

trans_df = trans.map_trans(genotype_df, phenotype_df, covariates_df, batch_size=10000, return_sparse=True, pval_threshold=1e-5, maf_threshold=0.01) trans_df = trans.filter_cis(trans_df, phenotype_pos_df, variant_df, window=5000000)

def apply_permutations(res, pairs_df): """ res: output from map_permutations() pairs_df: output from map_trans() """

if isinstance(res, pd.Series):  # chrs not split
    nperms = len(res['minp_true_df'])
    for k in ['beta_shape1', 'beta_shape2', 'true_df']:
        pairs_df[k] = res[k]
    pairs_df['pval_true_dof'] = pval_from_corr(pairs_df['r2'], pairs_df['true_df'])
    pairs_df['pval_perm'] = np.array([(np.sum(res['minp_empirical']<=p)+1)/(nperms+1) for p in pairs_df['pval']])
    pairs_df['pval_beta'] = stats.beta.cdf(pairs_df['pval_true_dof'], pairs_df['beta_shape1'], pairs_df['beta_shape2'])

[francois-a]

You need to add the argument return_r2=True to map_trans. I'll update the documentation — thanks for pointing this out!

[lintingyi2014]

thank you!!!