Package index • isotwas

Training models

Functions for training multivariate predictive models

compute_isotwas(): Compute isoTWAS model for a set of isoforms/transcripts

compute_mrce(): Multivariate regression with covariance estimate

compute_omega(): Compute precision matrix between isoforms

compute_blup(): Univariate BLUP on all columns

multivariate_elasticnet(): Multivariate elastic net on all columns with row-wise penalty

multivariate_joinet(): Multivariate stacked elastic net on all columns using joinet

multivariate_spls(): Multivariate sparse partial least squares

multivariate_graph_reg(): Multivariate Graph-Regularized Regression

multivariate_mtlasso(): Multivariate Multi-Task LASSO

multivariate_mtlasso_cv(): Multivariate Multi-Task LASSO with multiple regularization comparison

multivariate_sgl(): Multivariate Sparse Group LASSO

multivariate_sgl_cv(): Cross-validated Sparse Group LASSO with automatic alpha selection

multivariate_stacking(): Multivariate Super Learner Stacking

univariate_blup(): Univariate BLUP on all columns

univariate_elasticnet(): Univariate elastic net on all columns

univariate_susie(): Univariate SuSiE on all columns

convert_model(): Convert isotwas model list to tibble

convert_legacy_model(): Convert legacy model list to isotwas_model

Model objects

Functions for creating and working with isotwas model objects

create_isotwas_model(): isoTWAS Model Classes and Methods

create_isotwas_result(): Create an isotwas_result object

create_transcript_model(): Create a single transcript model entry

get_best_isotwas(): Select best model per transcript from multiple isotwas_model objects

get_prediction_matrix(): Get predicted values as a matrix

get_weight_matrix(): Get weights for all transcripts as a matrix

print(<isotwas_model>): Print method for isotwas_model

print(<isotwas_result>): Print method for isotwas_result

summary(<isotwas_model>): Summary method for isotwas_model

summary(<isotwas_result>): Summary method for isotwas_result

`$`(<isotwas_model>): Extract a transcript model from isotwas_model

`[`(<isotwas_model>): Subset isotwas_model by transcript name

Similarity from GTF

Functions for computing transcript similarity from GTF annotations

similarity_from_gtf(): Create Isoform Similarity Matrix from GTF

create_similarity_from_exons(): Create similarity matrix from shared exons

subset_similarity(): Create similarity matrix for a subset of transcripts

Trait mapping

Stage-wise trait mapping

p_screen(): Compute screening P-value for one gene

p_confirm(): Compute confirmation P-value for one gene

burdenTest(): Compute weighted burden test

burdenTest_all(): Run burden test on all transcripts in an isotwas_model

Probabilistic fine-mapping

Functions for FOCUS-like probabilistic fine-mapping

twas_finemap(): FOCUS-like gene-level finemapping

estimate_cor(): Compute correlation for fine-mapping

get_resid(): Compute residuals for Z-scores

bayes_factor(): Compute Bayes factors for TWAS Z-scores

conditional_test_focus(): Conditional gene-level test

conditional_test(): Conditional gene-level test