Man pages for liangyy/mixqtl
Combine total and allele-specific counts for cis-QTL analysis
| create_betas | Generate a beta vector |
| create_gene | Generate a gene instance for simulation |
| create_genotype | Generate genotype (for single SNP model only) |
| do_elastic_net | Adapted from... |
| fit_glmnet_with_cv | Wrapper for fitting elastic net model with nested... |
| get_permutations | Generate permutation matrix |
| impute_geno | Filling in missing genotype |
| matrix_ls_asc | ascQTL for nominal pass in matrix form |
| matrix_ls_asc_permutation | ascQTL with permutation in matrix form |
| matrix_ls_trc | trcQTL for nominal pass in matrix form |
| matrix_ls_trc_permutation | trcQTL with permutation in matrix form |
| matrixQTL_one_dim | Solve Y = Xb + e in matrix form |
| matrixQTL_two_dim | Solve Y = X1 b1 + X2 b2 + e in matrix form |
| matrixQTL_with_mask_one_dim | Solve Y = Xb + e with mask and weight in matrix form |
| matrixQTL_with_mask_two_dim | Solve Y = X1 b1 + X2 b2 + e with mask in matrix form |
| meta_analyze | Meta-analyze trcQTL and ascQTL results |
| mixfine | Combining total and allele-specific reads for fine-mapping |
| mixfine_old | Combining total and allele-specific reads for fine-mapping |
| mixpred | Combining total and allele-specific reads for building... |
| mixpred_old | Combining total and allele-specific reads for building... |
| mixqtl | Combining total and allele-specific reads for QTL mapping |
| regress_against_covariate | Regress against covariates for trcQTL |
| simulate_read_count | Simulate read count (single SNP model) |
| simulate_read_count_multi | Simulate read count (multi-SNP model) |
