Man pages for TheJacksonLaboratory/mousegwas
Run in-bred mouse GWAS
| average_strain | Return the beta of each strain. Strains are similar if... |
| calc_kinship | Call gemma to calculate kinship matrix |
| calc_pylmm_kinship | Calculate kinship using PyLMM |
| combine_metaSOFT | Combine phenotypes using metasoft |
| combine_metaSOFT_pylmm | Title |
| execute_lmm | Run lmm 2 (LRT) on the data with LOCO |
| get_gemma | Script for executing GEMMA and reading its output Download... |
| get_genes | Retrieve genes from biomaRt and return the intersecting genes |
| get_multi | Download MultiTrans |
| get_residuals | Get resudials of phenotypes Not used any more |
| get_sigmas | Extract Vg and Ve from GEMMA log file |
| get_sigmas_dep | Extract Vg and Ve from GEMMA log file |
| hello | Hello, World! |
| plot_gemma_lmm | Plot the GWAS results as a Manhattan plot and highlight... |
| rep_peaks | Find peaks and LD blocks in the LMM results |
| run_C | Run java generateC |
| run_emma | Run EMMA using the EMMA R package |
| run_inrich | Rnu KEGG and GO INRICH for written intervals |
| run_pylmm | Run pylmm |
| run_pylmm_exec | Run pyLMM for each phenotype and combine using metaSOFT |
| run_R | Wrap generateR.R |
| run_slide | Run SLIDE |
| write_genes_map | Write the genes, KEGG and GO mapping for INRICH execution |
| write_inrich_expression | Title |
| write_inrich_phenotype | Write the intervals for INRICH execution |
| write_inrich_snps | Write the SNPs map for INRICH execution |
