Merge pull request #12 from bschilder/Revised

Revised

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: ThreeWayTest
 Type: Package
-Title: packageTitle
-Version: 0.99.0
+Title: ThreeWayTest
+Version: 1.0.0
 Authors@R: c( 
-     person(given = "yourGivenName",
-           family = "yourFamilyName",
+     person(given = "Deliang",
+           family = "Bu",
            role = c("cre"),
-           email = "[email protected]",
-           comment = c(ORCID = "yourOrcidId"))
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-9939-5708"))
     )
 Description: Summary statistics-based association test for 
     identifying the pleiotropic effects with set of genetic variants.
@@ -17,10 +17,7 @@ Encoding: UTF-8
 Depends: R (>= 4.0.2)
 biocViews:
 Imports:
-    matlib,
     MASS,
-    MSKAT,
-    AssocTests
 Suggests:
     rworkflows,
     methods,

NAMESPACE

@@ -1,8 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
-export(calculate_stat_T3)
-export(myCCA)
-export(quadratic_test)
-export(standard_chisq)
-export(true_cov_mat_generation_autoregressive)
+export(MGAS)
+export(TWT)
+export(T_3)
+export(T_eta)
+export(approximate_distribution_coefficient_estimate_T3)
+export(chisq_test)
+export(coefficient_estimate)
+export(gen_autoregressive)
+export(generate_null_distribution_T3)
+export(metaCCA)
 importFrom(MASS,ginv)
+importFrom(MASS,mvrnorm)

R/data.R

@@ -1,8 +1,20 @@
 #' data_matrix_final
 #'
 #' @description
-#' matrix of real data.
-#' (expand description) 
+#' Data matrix of Polyunsaturated fatty acids in real data analysis。
+#' CHR is the chromesome number.
+#' SNP is the number of SNP.
+#' BP is the poisition of the SNP.
+#' ANNOT is gene that this SNP is annoted to.
+#' Other Allele is the  allele that counts as 0.
+#' Effect Allele is the allele that counts as 1.
+#' MAF is the allele frequency of other allele.
+#' The last 6 columns of wAA, wALA, wDHA, wEDA, wEPA and wLA is the 
+#' wald test statistics of 6 phenotypes: arachidonic acid, 
+#' alpha-linolenic acid, docosahexanoic acid, eicosadienoic acid
+#' and eicosapentanoic acid.
+#' For original data and more detailed data description, please visit:
+#' https://grasp.nhlbi.nih.gov/FullResults.aspx. The data is in Year 2009 (2).
 #' \code{
 #' load(file.path("data","data_matrix_final.Rdata"))
 #' usethis::use_data(data_matrix_final, overwrite = TRUE)
@@ -13,60 +25,68 @@
 #' covariance_matrix_data
 #'
 #' @description 
-#' The used data for calculating phenotype covariance gene list. 
-#' (expand description) 
+#' Part of Polyunsaturated fatty acids data after LD pruning to calculate 
+#' phenotype covariance matrix. Detailed description is the same as 
+#' data_matrix_final. 
 #' \code{
 #' load(file.path("data","covariance_matrix_estimated.Rdata"))
 #' usethis::use_data(covariance_matrix_data, overwrite = TRUE)
 #' }
 #' @usage data("covariance_matrix_data")
 "covariance_matrix_data"
 
-#' final_1kg_genotype_correct_sub
+#' selected_genotype
 #'
 #' @description 
-#' Note that the full \emph{final_1kg_genotype_correct.Rdat} is not 
-#' uploaded because of the size. Here we upload one part-version of this data
-#' \emph{final_1kg_genotype_correct_sub.Rdata} and 
-#' a document on how to access the full data. 
-#' (add description) 
+#' 2504 samples in 1000 genomes project for 
+#' calculating covariance matrix of genotypes.
+#' CHR is the chromesome number.
+#' SNP is the number of SNP.
+#' BP is the poisition of the SNP.
+#' Counted is the  allele that counts as 1.
+#' ALT is the allele that counts as 0.
+#' Due to R package limit of data, this is a part-version with 9 SNPs of gene
+#' FADS2 to run getting_start.R in the vigneets.
+#' For full Data, Please go https://github.com/bschilder/ThreeWayTest.
 #' \code{
-#' load(file.path("data","final_1kg_genotype_correct_sub.Rdata"))
-#' usethis::use_data(final_1kg_genotype_correct_sub, overwrite = TRUE)
+#' load(file.path("data","selected_genotype.Rdata"))
+#' usethis::use_data(selected_genotype, overwrite = TRUE)
 #' }
-#' @usage data("final_1kg_genotype_correct_sub")
-"final_1kg_genotype_correct_sub"
-
-#' gene_length_list
-#'
-#' @description 
-#' (add description) 
-#' \code{
-#' load(file.path("data","gene_length_list.Rdata"))
-#' usethis::use_data(gene_length_list, overwrite = TRUE)
-#' }
-#' @usage data("gene_length_list")
-"gene_length_list"
+#' @usage data("selected_genotype")
+"selected_genotype"
 
 #' gene_list
 #'
 #' @description 
-#' (add description) 
+#' List of gene names for performing real data analysis.
 #' \code{
 #' load(file.path("data","gene_list.Rdata"))
 #' usethis::use_data(gene_list, overwrite = TRUE)
 #' }
 #' @usage data("gene_list")
 "gene_list"
 
-#' snpinfo_12
+#' gene_length_list
+#'
+#' @description 
+#' Number of SNPs contains in each gene.
+#' \code{
+#' load(file.path("data","gene_length_list.Rdata"))
+#' usethis::use_data(gene_length_list, overwrite = TRUE)
+#' }
+#' @usage data("gene_length_list")
+"gene_length_list"
+
+#' PCA_result
 #'
 #' @description 
-#' (add description) 
+#' Principle components for population stratification used as 
+#' covariates in regression model. Here we use PCA_result$principal.coordinates
+#' as the covariates in our regression model.
 #' \code{
-#' snpinfo_12 <- read.table(file.path("data","snpinfo_12.txt"), header = FALSE)
-#' usethis::use_data(snpinfo_12, overwrite = TRUE)
+#' load(file.path("data","PCA_result.Rdata"))
+#' usethis::use_data(PCA_result, overwrite = TRUE)
 #' }
-#' @usage data("snpinfo_12")
-"snpinfo_12" 
+#' @usage data("PCA_result")
+"PCA_result"