Penalized Linear Mixed Models for Correlated Data
A helper function to add predictors to a filebacked matrix of data
A helper function to support process_plink()
a version of cbind() for file-backed matrices
check_for_file_extension: a function to make our package 'smart' enoug...
Coef method for "cv_plmm" class
Coef method for "plmm" class
a function to create the estimated variance matrix from a PLMM fit
A helper function to count constant features
A helper function to count the number of cores available on the curren...
A function to create a design matrix, outcome, and penalty factor to b...
A function to create a design with an in-memory X matrix
a function to create a design for PLMM modeling
create_log_file
Cross-validation for plmm
Cross-validation internal function for cv_plmm
A function to take the eigendecomposition of K Note: This is faster th...
Estimate eta (to be used in rotating the data) This function is called...
Functions to convert between FBM and big.matrix type objects
A function to help with accessing example PLINK files
Read in processed data This function is intended to be called after ei...
a function to return the computer's host name
A function to impute SNP data
A function to align genotype and phenotype data
Generate nicely formatted lambda vec
helper function to implement lasso penalty
Evaluate the negative log-likelihood of an intercept-only Gaussian plm...
helper function to implement MCP penalty The helper functions to imple...
A helper function to label and summarize the contents of a bigSNP
plmm_checks
PLMM fit: a function that fits a PLMM using the values returned by plm...
PLMM format: a function to format the output of a model constructed wi...
Loss method for "plmm" class
PLMM prep: a function to run checks, SVD, and rotation prior to fittin...
Fit a linear mixed model via penalized maximum likelihood.
plmmr: Penalized Linear Mixed Models for Correlated Data
Plot method for cv_plmm class
Plot method for plmm class
Predict method to use in cross-validation (within cvf)
Predict method for plmm class
a function to format the time
Print method for summary.cv_plmm objects
A function to print the summary of a plmm model
A function to read in large data files as an FBM
Preprocess PLINK files using the bigsnpr package
A function to read in a large file as a numeric file-backed matrix (`F...
A function to read in PLINK files using bigsnpr methods
Calculate a relatedness matrix
A function to rotate filebacked data
helper function to implement SCAD penalty
Compute sequence of lambda values
A helper function to standardize a filebacked matrix
A helper function to standardize matrices
A helper function to subset big.matrix objects
A summary function for cv_plmm objects
A summary method for the plmm objects
Untransform coefficient values back to the original scale for file-bac...
Untransform coefficient values back to the original scale *In memory...
Untransform coefficient values back to the original scale for file-bac...
Untransform coefficient values back to the original scale
For Linux/Unix and MacOS only, here is a companion function to unzip t...
Fits penalized linear mixed models that correct for unobserved confounding factors. 'plmmr' infers and corrects for the presence of unobserved confounding effects such as population stratification and environmental heterogeneity. It then fits a linear model via penalized maximum likelihood. Originally designed for the multivariate analysis of single nucleotide polymorphisms (SNPs) measured in a genome-wide association study (GWAS), 'plmmr' eliminates the need for subpopulation-specific analyses and post-analysis p-value adjustments. Functions for the appropriate processing of 'PLINK' files are also supplied. For examples, see the package homepage. <https://pbreheny.github.io/plmmr/>.