Original routine used in vignette. Want to move most of this to using cmst_default
.
cmst cmst1 fitFunction model_setup calcICs calcZ normIUCMST binomIUCMST normJointIUCMST model_setup
Routine now used in R/qtl2shiny: mediate1_test
mediation_test
cmst_pheno
cmst_default
med_fits
fitFunction
combo_models
combine_models
testFunction <- wilcIUCMST, binomIUCMST, normJointIUCMST, normIUCMST
calcZ
calcICs
calcShat
left_right
mediation_triad med_fits fitFunction label_fn = qtl2pattern::pattern_label group_fn = qtl2pattern::pattern_sdp
Utilities
fitQtl2 uses qtl2::fit1 common_data (from qtl2pattern) covar_df_mx (from qtl2pattern) wh_sex(from qtl2pattern)
med_name <- sum_med$id[1] mediator <- med_ls[[1]][, med_name, drop = FALSE] driver_name <- (med_ls[[2]] %>% filter(id == med_name))$driver driver <- driver_med[,, driver_name]
sdp <- snpprobs_obj$snpinfo$sdp[which.min(abs(snpprobs_obj$snpinfo$pos - sum_med$pos[1]))]
scat_dat <- CausalMST::mediation_triad( target = pheno_data, mediator = mediator, driver = driver, covar_tar = covar, covar_med = med_ls$covar, kinship = kinship[[1]], sdp = sdp, allele = TRUE)
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