Man pages for dcgerard/vicar
Various Ideas for Confounder Adjustment in Regression

adjust_by_tReturns adjusted sebetahat's based on t likelihood so that we...
ash_ruv2Use control genes to estimate hidden confounders and variance...
ash_ruv4Use control genes to estimate hidden confounders and variance...
ash_wrapWrapper for 'ash.workhorse' for use in 'caw'.
back_elboThe Evidence lower bound.
back_fixFixed point iteration for BACKWASH.
back_objObjective function for BACKWASH.
back_update_phiUpdate for the "g" hyperparameter.
back_update_piUpdate for the prior mixing proportions.
back_update_qbetaUpdate for the variational density of beta
back_update_vUpdate for the variational density of v.
back_update_xiUpdate for the variance scaling parameter.
backwashBACKWASH: Bayesian Adjustment for Confounding Knitted With...
backwash_second_stepSecond step of the backwash procedure.
bfa_gd_gibbsFast Gibbs sampler for Bayesian factor analysis.
bfa_gsBayesian factor analysis used in Gerard and Stephens (2016).
bfa_gs_linkedSimple Bayesian low rank matrix decomposition.
bfa_gs_linked_gibbsFast Gibbs sampler for Bayesian factor analysis.
bfa_gs_linked_gibbs_rR implementation of 'bfa_gs_linked_gibbs'.
bfa_wrapperWrapper for the bfa package.
bflSimple Bayesian low rank matrix decomposition.
brent_obj_normObjective function for updating variance inflation parameter...
bsvdGibbs sampler for Bayesian SVD.
calc_lfsrEmpirical estimate of lfsr based on posterior samples.
calc_lfsr_gSame as 'calc_lfsr' except with a prior specification.
calc_mean_gCalculate moments of pointmass rv's.
calc_quantiles_gCalculate quantiles of pointmass rv's.
cawIterative procedure for confounder correction with a...
clean_my_pUse the distribution of control genes' p-values to adjust all...
clean_my_statsQuantile normalize stats to their theoretical distributions.
cruv4RUV4's second step.
cruv4_multicovRUV4's second step.
dnormalmixDensity of a mixture of normals
dt_wrapWrapper for dt with a non-zero mean and non-1 scale...
em_missEM algorithm for factor analysis with missing block matrix.
em_miss_fixFixed point iteration for em algorithm with missing block.
em_miss_fix_fastFaster version of 'em_miss_fix'.
em_miss_objThe objective function for em with a missing block.
em_miss_obj_fastA faster version of em_miss_obj.
fa_mlWrapper for cate's fa.em function.
fa_out_testTest output form fa_func.
fa_testerTests whether a user-specified factor analysis function is...
fa_tester_ruvbTest whether a user-specified function is compatible with...
fix_cawA fixed point iteration for CAW.
fix_caw_wrapperA wrapper for 'fix_caw' so that I can use SQUAREM.
gdfaOld version of Bayesian factor analysis.
get_grid_varDefault way to set grid of variances.
hard_imputeMy version of hard imputation that begins at the ruv...
hier_funHierarchical prior density function as described in Gerard...
impute_blockConstructs an overall matrix, then applies a given imputation...
impute_ruv_reproduceReproduce RUV2, RUV3, and RUV4 with RUVimpute.
initialize_mixing_propFunction for initializing mixing proportions.
knn_wrapperWrapper for impute.knn
missforest_wrapperWrapper for missForest package.
mouthwashMOUTHWASH: Maximize Over Unobservables To Help With Adaptive...
mouthwash_coordinateCoordinate ascent for optimizing t likelihood with uniform...
mouthwash_second_stepThe second step of MOUTHWASH.
mouthwash_z_gradGradient wrt z of 'uniform_mix_llike'.
normal_mix_fixA fixed point iteration for updating the mixing proportions...
normal_mix_fix_wrapperWrapper for 'normal_mix_fix' so that I can use SQUAREM.
normal_mix_llikePenalized MOUTHWASH likelihood when using a mixture of...
normal_mix_llike_wrapperWrapper for 'normal_mix_llike' so that I can use it in...
normal_priorA basic normal prior density function.
pca_2stepPCA when first 'vr' rows have a variance multiplicatively...
pca_naiveBasic PCA.
pca_ruv2PCA when first 'vr' rows have a variance multiplicatively...
pcaruv2_fixFix point for mle in pca_ruv2.
pcaruv2_objThe objective function for mle in pca_ruv2.
plot.backwashPlotting method for 'backwash'.
plot.mouthwashPlotting method for 'moutwash'.
plot.ruvbPlotting method for 'ruvb'.
prior_fun_wrapperWrapper for 'prior_fun' so that can be called in apply.
ptdiffMore stable way to calculate differences in T cdf's.
ptdiff_matMore stable way to calculate differences in T cdfs when input...
ptdiff_mat_logLog version of 'ptdiff_mat'.
pt_wrapWrapper for pt with a non-zero mena and non-1 scale...
qmle_objObjective function for quasi-mle approach.
qmle_obj_basicBasic no optimized code objective function.
qmle_ruv2Quasi-mle when first 'vr' rows of 'Y' have variances which...
qmle_ruv2_lambda_gridQuasi-mle when first 'vr' rows of 'Y' have variances which...
qr_identAn identified QR decomposition.
rmixnormDraw from a mixture of normals.
rnormalmixRandom draw from a mixture of normals.
rotate_modelQR rotation to independent models.
rubin_copyVery inneficient copy of rubin and thayer iteration mostly...
ruv3Removing Unwanted Variation 3.
ruvbBayesian version of Removing Unwanted Variation.
ruvemSame as ruvimpute but only does ruvem and comes up with...
ruvimputeGeneral imputation framework.
sim_gtexA simulated RNA-seq dataset.
smell_my_pWrapper for a Kolmogorov-Smirnov test using the p-values from...
smell_my_statsWrapper for a Kolmogorov-Smirnov test using the statistics...
softimpute_wrapperA wrapper for using the softImpute function from the...
tregress_emEM algorithm to find regression coefficients using...
tregress_fixFixed point iteration for EM algorithm for regression with...
tregress_objThe likelihood for regression with t-errors where the...
tregress_obj_wrapperWrapper for 'tregress_obj'.
unif_int_gradGradient wrt z2 of intermediate function in EM.
unif_int_objIntermediate objective function in EM.
uniform_mix_fixFixed point iteration when using t errors and a mixture of...
uniform_mix_fix_wrapperWrapper for 'uniform_mix_fix', mostly so I can use SQUAREM.
uniform_mix_llikeLog-likelihood when using t errors and mixture of uniforms...
uniform_mix_llike_wrapperWrapper for 'uniform_mix_llike', mostly for the SQUAREM...
update_fUtility function for updating F in 'gdfa'.
update_lambdaWrapper for 'optim' and 'qmle_obj'.
update_sig_alphaFast update for sig_diag and alpha.
update_sig_alpha_basicBasic no optimized code update for sig_diag and alpha.
vicar'vicar': Various Ideas for Confounder Adjustment in...
vruv2Calibrated RUV2.
vruv2_oldOld version of Calibrated RUV2 that doesn't really work.
vruv4Calibrated RUV4 where the control genes are used to estimate...
vruvinvVariance inflated RUV-inverse.
dcgerard/vicar documentation built on Oct. 31, 2017, 7:42 a.m.