Error checks and plotting speedups for dive_phe2mash function

This commit is contained in:
2021-03-31 18:17:02 -05:00
parent 027323acf6
commit 1edd72d15e
26 changed files with 779 additions and 63 deletions

View File

@@ -11,25 +11,44 @@ export(dive_phe2mash)
export(enquo)
export(enquos)
export(expr)
export(get_GxE)
export(get_U_by_mass)
export(get_lambdagc)
export(get_pairwise_sharing)
export(get_qqplot)
export(get_significant_results)
export(mash_plot_Ulist)
export(mash_plot_covar)
export(mash_plot_manhattan_by_condition)
export(mash_plot_marker_effect)
export(mash_plot_pairwise_sharing)
export(mash_plot_sig_by_condition)
export(sym)
export(syms)
import(bigsnpr)
import(bigstatsr)
import(ggplot2)
import(mashr)
importFrom(GGally,ggcorr)
importFrom(ashr,get_fitted_g)
importFrom(ashr,get_lfsr)
importFrom(ashr,get_pm)
importFrom(ashr,get_psd)
importFrom(bigassertr,printf)
importFrom(bigsnpr,snp_autoSVD)
importFrom(cluster,daisy)
importFrom(cowplot,save_plot)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
@@ -52,11 +71,15 @@ importFrom(rlang,enquos)
importFrom(rlang,expr)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(rlist,list.append)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,ppoints)
importFrom(stats,predict)
importFrom(stats,qbeta)
importFrom(stats,uniroot)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(tibble,add_column)
importFrom(tibble,add_row)
importFrom(tibble,as_tibble)
@@ -64,6 +87,8 @@ importFrom(tibble,enframe)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyselect,all_of)
importFrom(utils,tail)