Documentation for fit_hlmm_model.py script¶
This script fits a heteroskedastic linear model (HLMs) (hetlm.model) or heteroskedastic linear mixed model (HLMMs) (hetlmm.model) to a given response (phenotype), mean covariates,
variance covariates, and variables to model random effects for.
The phenotype (response) file and covariate file formats are the same: plain text files with at least three columns. The first column is family ID, and the second column is individual ID; subsequent columns are phenotype or covariate observations. This is the same format used by GCTA and FaSTLMM.
If you specify a random_gts.bed file with the option –random_gts, the script will fit a HLMM (hetlmm.model),
modelling random effects for the SNPs in random_gts.bed. If no –random_gts are specified, then a HLM (hetlm.model)
is used, without random effects. If you add the flag –random_gts_txt, the program assumes that the file
specified for –random_gts is a text file formatted as: FID, IID, x1, x2, …
If mean and/or variance covariates are specified, the script will output two files: outprefix.mean_effects.txt, containing the estimated mean effects and their standard errors; and outprefix.variance_effects.txt, containing the estimated log-linear variance effects and their standard errors.
If –random_gts are specified, the script will output an estimate of the variance of the random effects in outprefix.h2.txt. –no_h2_estimate suppresses this output.
Arguments
Required positional arguments:
- phenofile
- Location of the phenotype (response) file with format: FID, IID, y1, y2, …
- outprefix
- Location to output csv file with association statistics
Options:
| --mean_covar | Location of mean covariate file (default no mean covariates) |
| --var_covar | Locaiton of variance covariate file (default no variance covariates) |
| --random_gts | Location of the BED file with the genotypes of the SNPs that random effects should be modelled for. If
random_gts are provided, HLMMs (hetlmm.model) are fit, rather than HLMs (hetlm.model). |
| --random_gts_txt | |
| If this flag is specified, the program assumes the file specified in for –random_gts is formatted as a text file with at least three columns: FID, IID, x1, x2, … | |
| --h2_init | Initial value for variance explained by random effects (default 0.05) |
| --phen_index | If the phenotype file contains multiple phenotypes, specify the phenotype to analyse. Default is first phenotype in file. Index counts starting from 1, the first phenotype in the phenotye file. |
| --missing_char | Missing value string in phenotype file (default NA) |
| --no_h2_estimate | |
| Suppress output of h2 estimate | |
Example Usage
We recommend working through the tutorial (Tutorial) to learn how to use hlmm_chr.py. The usage of this script is similar, if a little simpler.