diff --git a/DESCRIPTION b/DESCRIPTION index 8bd353c..3f61397 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: STAARpipelineSummary Type: Package Title: Summarization and Visualization of Analysis Results Generated by STAARpipeline Version: 0.9.7 -Date: 2023-11-11 +Date: 2024-03-23 Author: Xihao Li [aut, cre], Zilin Li [aut, cre] Maintainer: Xihao Li , Zilin Li Description: An R package for summarizing analysis results generated by STAARpipeline. diff --git a/R/Gene_Centric_Coding_Results_Summary.R b/R/Gene_Centric_Coding_Results_Summary.R index f2894a0..c640cde 100644 --- a/R/Gene_Centric_Coding_Results_Summary.R +++ b/R/Gene_Centric_Coding_Results_Summary.R @@ -24,16 +24,11 @@ #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; #' \code{naive} refers to regressing residuals from the null model on \code{known_loci} #' and taking the residuals (default = \code{optimal}). -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). -#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). -#' @param method_cond a character value indicating the method for conditional analysis. -#' \code{optimal} refers to regressing residuals from the null model on \code{known_loci} -#' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; -#' \code{naive} refers to regressing residuals from the null model on \code{known_loci} -#' and taking the residuals (default = \code{optimal}). #' @param rare_maf_cutoff the cutoff of maximum minor allele frequency in #' defining rare variants (default = 0.01). #' @param QC_label channel name of the QC label in the GDS/aGDS file (default = "annotation/filter"). +#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param Annotation_dir channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation"). #' @param Annotation_name_catalog a data frame containing the name and the corresponding channel name in the aGDS file. #' @param Use_annotation_weights use annotations as weights or not (default = FALSE). @@ -79,7 +74,7 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_jobs_num,input_path,output_path,gene_centric_results_name, obj_nullmodel,known_loci=NULL,cMAC_cutoff=0, method_cond=c("optimal","naive"),rare_maf_cutoff=0.01, - QC_label="annotation/filter",geno_missing_imputation=c("mean","minor"),variant_type=c("SNV","Indel","variant"), + QC_label="annotation/filter",variant_type=c("SNV","Indel","variant"),geno_missing_imputation=c("mean","minor"), Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog, Use_annotation_weights=FALSE,Annotation_name=NULL, alpha=2.5E-06,manhattan_plot=FALSE,QQ_plot=FALSE, diff --git a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R index 2bae220..e7095a0 100644 --- a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R +++ b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R @@ -24,16 +24,11 @@ #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; #' \code{naive} refers to regressing residuals from the null model on \code{known_loci} #' and taking the residuals (default = \code{optimal}). -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). -#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). -#' @param method_cond a character value indicating the method for conditional analysis. -#' \code{optimal} refers to regressing residuals from the null model on \code{known_loci} -#' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; -#' \code{naive} refers to regressing residuals from the null model on \code{known_loci} -#' and taking the residuals (default = \code{optimal}). #' @param rare_maf_cutoff the cutoff of maximum minor allele frequency in #' defining rare variants (default = 0.01). #' @param QC_label channel name of the QC label in the GDS/aGDS file (default = "annotation/filter"). +#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param Annotation_dir channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation"). #' @param Annotation_name_catalog a data frame containing the name and the corresponding channel name in the aGDS file. #' @param Use_annotation_weights use annotations as weights or not (default = FALSE). @@ -83,14 +78,14 @@ #' @export Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_coding_jobs_num,input_path,output_path,gene_centric_results_name, - obj_nullmodel,known_loci=NULL,cMAC_cutoff=0, - method_cond=c("optimal","naive"),rare_maf_cutoff=0.01, - QC_label="annotation/filter",geno_missing_imputation=c("mean","minor"),variant_type=c("SNV","Indel","variant"), - Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog, - Use_annotation_weights=FALSE,Annotation_name=NULL, - alpha=2.5E-06,manhattan_plot=FALSE,QQ_plot=FALSE, - cond_null_model_name=NULL,cond_null_model_dir=NULL, - SPA_p_filter=FALSE,p_filter_cutoff=0.05){ + obj_nullmodel,known_loci=NULL,cMAC_cutoff=0, + method_cond=c("optimal","naive"),rare_maf_cutoff=0.01, + QC_label="annotation/filter",variant_type=c("SNV","Indel","variant"),geno_missing_imputation=c("mean","minor"), + Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog, + Use_annotation_weights=FALSE,Annotation_name=NULL, + alpha=2.5E-06,manhattan_plot=FALSE,QQ_plot=FALSE, + cond_null_model_name=NULL,cond_null_model_dir=NULL, + SPA_p_filter=FALSE,p_filter_cutoff=0.05){ ## evaluate choices method_cond <- match.arg(method_cond) diff --git a/R/Gene_Centric_Noncoding_Results_Summary.R b/R/Gene_Centric_Noncoding_Results_Summary.R index bda539b..5d1055c 100644 --- a/R/Gene_Centric_Noncoding_Results_Summary.R +++ b/R/Gene_Centric_Noncoding_Results_Summary.R @@ -27,16 +27,11 @@ #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; #' \code{naive} refers to regressing residuals from the null model on \code{known_loci} #' and taking the residuals (default = \code{optimal}). -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). -#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). -#' @param method_cond a character value indicating the method for conditional analysis. -#' \code{optimal} refers to regressing residuals from the null model on \code{known_loci} -#' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; -#' \code{naive} refers to regressing residuals from the null model on \code{known_loci} -#' and taking the residuals (default = \code{optimal}). #' @param rare_maf_cutoff the cutoff of maximum minor allele frequency in #' defining rare variants (default = 0.01). #' @param QC_label channel name of the QC label in the GDS/aGDS file (default = "annotation/filter"). +#' @param variant_type type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param Annotation_dir channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation"). #' @param Annotation_name_catalog a data frame containing the name and the corresponding channel name in the aGDS file. #' @param Use_annotation_weights use annotations as weights or not (default = FALSE). @@ -92,7 +87,7 @@ Gene_Centric_Noncoding_Results_Summary <- function(agds_dir,gene_centric_noncodi ncRNA_jobs_num,ncRNA_input_path,ncRNA_output_path,ncRNA_results_name, obj_nullmodel,known_loci=NULL,cMAC_cutoff=0, method_cond=c("optimal","naive"),rare_maf_cutoff=0.01, - QC_label="annotation/filter",geno_missing_imputation=c("mean","minor"),variant_type=c("SNV","Indel","variant"), + QC_label="annotation/filter",variant_type=c("SNV","Indel","variant"),geno_missing_imputation=c("mean","minor"), Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog, Use_annotation_weights=FALSE,Annotation_name=NULL, alpha=2.5E-06,alpha_ncRNA=2.5E-06, diff --git a/R/Individual_Analysis_Results_Summary.R b/R/Individual_Analysis_Results_Summary.R index e8f3ecd..f70bea4 100644 --- a/R/Individual_Analysis_Results_Summary.R +++ b/R/Individual_Analysis_Results_Summary.R @@ -21,8 +21,9 @@ #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; #' \code{naive} refers to regressing residuals from the null model on \code{known_loci} #' and taking the residuals (default = \code{optimal}). -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param QC_label channel name of the QC label in the GDS/aGDS file. +#' @param variant_type type of variant included in the analysis. Choices include "variant", "SNV", or "Indel" (default = "variant"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param alpha p-value threshold of significant results (default = 5E-09). #' @param manhattan_plot output manhattan plot or not (default = FALSE). #' @param QQ_plot output Q-Q plot or not (default = FALSE). @@ -44,7 +45,7 @@ Individual_Analysis_Results_Summary <- function(agds_dir,jobs_num,input_path,output_path,individual_results_name, obj_nullmodel,known_loci=NULL, method_cond=c("optimal","naive"), - QC_label="annotation/filter",geno_missing_imputation=c("mean","minor"), + QC_label="annotation/filter",variant_type=c("variant","SNV","Indel"),geno_missing_imputation=c("mean","minor"), alpha=5E-09,manhattan_plot=FALSE,QQ_plot=FALSE, SPA_p_filter=FALSE,p_filter_cutoff=0.05, cond_null_model_name=NULL,cond_null_model_dir=NULL){ @@ -183,9 +184,9 @@ Individual_Analysis_Results_Summary <- function(agds_dir,jobs_num,input_path,out gds.path <- agds_dir[chr] genofile <- seqOpen(gds.path) - results_sig_cond_chr <- Individual_Analysis_cond(chr=chr,individual_results=results_sig_chr,genofile,obj_nullmodel=obj_nullmodel, - known_loci=known_loci,variant_type="variant", - QC_label=QC_label,geno_missing_imputation=geno_missing_imputation,method_cond=method_cond) + results_sig_cond_chr <- Individual_Analysis_cond(chr=chr,individual_results=results_sig_chr,genofile=genofile,obj_nullmodel=obj_nullmodel, + known_loci=known_loci,method_cond=method_cond,QC_label=QC_label, + variant_type=variant_type,geno_missing_imputation=geno_missing_imputation) results_sig_cond <- rbind(results_sig_cond,results_sig_cond_chr) @@ -210,8 +211,8 @@ Individual_Analysis_Results_Summary <- function(agds_dir,jobs_num,input_path,out obj_nullmodel_cond <- get(load(paste0(cond_null_model_dir,cond_null_model_name,".chr",chr,".Rdata"))) - results_sig_cond_chr <- Individual_Analysis_cond_spa(chr=chr,individual_results=results_sig_chr,genofile,obj_nullmodel=obj_nullmodel_cond, - variant_type="variant",QC_label=QC_label,geno_missing_imputation=geno_missing_imputation, + results_sig_cond_chr <- Individual_Analysis_cond_spa(chr=chr,individual_results=results_sig_chr,genofile=genofile,obj_nullmodel=obj_nullmodel_cond, + QC_label=QC_label,variant_type=variant_type,geno_missing_imputation=geno_missing_imputation, SPA_p_filter=SPA_p_filter,p_filter_cutoff=p_filter_cutoff) results_sig_cond <- rbind(results_sig_cond,results_sig_cond_chr) @@ -224,8 +225,8 @@ Individual_Analysis_Results_Summary <- function(agds_dir,jobs_num,input_path,out gds.path <- agds_dir[chr] genofile <- seqOpen(gds.path) - results_sig_cond_chr <- Individual_Analysis_cond_spa(chr=chr,individual_results=results_sig_chr,genofile,obj_nullmodel=obj_nullmodel, - variant_type="variant",QC_label=QC_label,geno_missing_imputation=geno_missing_imputation, + results_sig_cond_chr <- Individual_Analysis_cond_spa(chr=chr,individual_results=results_sig_chr,genofile=genofile,obj_nullmodel=obj_nullmodel, + QC_label=QC_label,variant_type=variant_type,geno_missing_imputation=geno_missing_imputation, SPA_p_filter=SPA_p_filter,p_filter_cutoff=p_filter_cutoff) results_sig_cond <- rbind(results_sig_cond,results_sig_cond_chr) diff --git a/R/Single_Variants_List_Analysis.R b/R/Single_Variants_List_Analysis.R index 3b49145..43a3511 100644 --- a/R/Single_Variants_List_Analysis.R +++ b/R/Single_Variants_List_Analysis.R @@ -8,8 +8,8 @@ #' the following names: "CHR" (chromosome number), "POS" (position), "REF" (reference allele), and "ALT" (alternative allele). #' @param obj_nullmodel an object from fitting the null model, which is either the output from \code{fit_nullmodel} function in the \code{STAARpipeline} package, #' or the output from \code{fitNullModel} function in the \code{GENESIS} package and transformed using the \code{genesis2staar_nullmodel} function in the \code{STAARpipeline} package. -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param QC_label channel name of the QC label in the GDS/aGDS file (default = "annotation/filter"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param p_filter_cutoff threshold for the p-value recalculation using the SPA method (default = 0.05) #' @param tol a positive number specifying tolerance, the difference threshold for parameter #' estimates in saddlepoint approximation algorithm below which iterations should be stopped (default = ".Machine$double.eps^0.25"). diff --git a/R/Sliding_Window_Results_Summary.R b/R/Sliding_Window_Results_Summary.R index b13a560..6a74e99 100644 --- a/R/Sliding_Window_Results_Summary.R +++ b/R/Sliding_Window_Results_Summary.R @@ -23,16 +23,11 @@ #' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; #' \code{naive} refers to regressing residuals from the null model on \code{known_loci} #' and taking the residuals (default = \code{optimal}). -#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). -#' @param variant_type variants include in the conditional analysis. Choices include "variant", "SNV", or "Indel" (default = "SNV"). -#' @param method_cond a character value indicating the method for conditional analysis. -#' \code{optimal} refers to regressing residuals from the null model on \code{known_loci} -#' as well as all covariates used in fitting the null model (fully adjusted) and taking the residuals; -#' \code{naive} refers to regressing residuals from the null model on \code{known_loci} -#' and taking the residuals (default = \code{optimal}). #' @param rare_maf_cutoff the cutoff of maximum minor allele frequency in #' defining rare variants (default = 0.01). #' @param QC_label channel name of the QC label in the GDS/aGDS file (default = "annotation/filter"). +#' @param variant_type variants include in the conditional analysis. Choices include "variant", "SNV", or "Indel" (default = "SNV"). +#' @param geno_missing_imputation method of handling missing genotypes. Either "mean" or "minor" (default = "mean"). #' @param Annotation_dir channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation"). #' @param Annotation_name_catalog a data frame containing the name and the corresponding channel name in the aGDS file. #' @param Use_annotation_weights use annotations as weights or not (default = FALSE). @@ -58,7 +53,7 @@ Sliding_Window_Results_Summary <- function(agds_dir,jobs_num,input_path,output_path,sliding_window_results_name, obj_nullmodel,known_loci=NULL,cMAC_cutoff=0, method_cond=c("optimal","naive"),rare_maf_cutoff=0.01, - QC_label="annotation/filter",geno_missing_imputation=c("mean","minor"),variant_type=c("SNV","Indel","variant"), + QC_label="annotation/filter",variant_type=c("SNV","Indel","variant"),geno_missing_imputation=c("mean","minor"), Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog, Use_annotation_weights=FALSE,Annotation_name=NULL, alpha=0.05,manhattan_plot=FALSE,QQ_plot=FALSE, diff --git a/R/manhattan_plot.R b/R/manhattan_plot.R index cebc89f..643a8d3 100644 --- a/R/manhattan_plot.R +++ b/R/manhattan_plot.R @@ -2,8 +2,8 @@ manhattan_plot<-function(chr, pos, pvalue, sig.level=NA, annotate=NULL, ann.default=list(), should.thin=T, thin.pos.places=2, thin.logp.places=2, xlab="Chromosome", ylab=expression(-log[10](p-value)), - col=c("gray","darkgray"), panel.extra=NULL, pch=20, - use_logp=FALSE,cex=0.8,...) { + col=c("gray","darkgray"), panel.extra=NULL, pch=20, + use_logp=FALSE,cex=0.8,...) { if (length(chr)==0) stop("chromosome vector is empty") if (length(pos)==0) stop("position vector is empty") diff --git a/README.md b/README.md index 3a2471b..5f2ae33 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ Please see the **STAARpipelineSum ## Data Availability The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the [Functional Annotation of Variant - Online Resource (FAVOR)](https://favor.genohub.org) site and [FAVOR Essential Database](https://doi.org/10.7910/DVN/1VGTJI). ## Version -The current version is 0.9.7 (January 29, 2024). +The current version is 0.9.7 (March 23, 2024). ## Citation If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite: diff --git a/docs/STAARpipelineSummary_manual.pdf b/docs/STAARpipelineSummary_manual.pdf index 34b8dc7..1f34eb5 100644 Binary files a/docs/STAARpipelineSummary_manual.pdf and b/docs/STAARpipelineSummary_manual.pdf differ diff --git a/man/Gene_Centric_Coding_Results_Summary.Rd b/man/Gene_Centric_Coding_Results_Summary.Rd index 5e18e4d..f6d929d 100644 --- a/man/Gene_Centric_Coding_Results_Summary.Rd +++ b/man/Gene_Centric_Coding_Results_Summary.Rd @@ -17,8 +17,8 @@ Gene_Centric_Coding_Results_Summary( method_cond = c("optimal", "naive"), rare_maf_cutoff = 0.01, QC_label = "annotation/filter", - geno_missing_imputation = c("mean", "minor"), variant_type = c("SNV", "Indel", "variant"), + geno_missing_imputation = c("mean", "minor"), Annotation_dir = "annotation/info/FunctionalAnnotation", Annotation_name_catalog, Use_annotation_weights = FALSE, @@ -64,10 +64,10 @@ defining rare variants (default = 0.01).} \item{QC_label}{channel name of the QC label in the GDS/aGDS file (default = "annotation/filter").} -\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} - \item{variant_type}{type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV").} +\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} + \item{Annotation_dir}{channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation").} \item{Annotation_name_catalog}{a data frame containing the name and the corresponding channel name in the aGDS file.} diff --git a/man/Gene_Centric_Coding_Results_Summary_incl_ptv.Rd b/man/Gene_Centric_Coding_Results_Summary_incl_ptv.Rd index 6b56474..a3fb8a5 100644 --- a/man/Gene_Centric_Coding_Results_Summary_incl_ptv.Rd +++ b/man/Gene_Centric_Coding_Results_Summary_incl_ptv.Rd @@ -17,8 +17,8 @@ Gene_Centric_Coding_Results_Summary_incl_ptv( method_cond = c("optimal", "naive"), rare_maf_cutoff = 0.01, QC_label = "annotation/filter", - geno_missing_imputation = c("mean", "minor"), variant_type = c("SNV", "Indel", "variant"), + geno_missing_imputation = c("mean", "minor"), Annotation_dir = "annotation/info/FunctionalAnnotation", Annotation_name_catalog, Use_annotation_weights = FALSE, @@ -64,10 +64,10 @@ defining rare variants (default = 0.01).} \item{QC_label}{channel name of the QC label in the GDS/aGDS file (default = "annotation/filter").} -\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} - \item{variant_type}{type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV").} +\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} + \item{Annotation_dir}{channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation").} \item{Annotation_name_catalog}{a data frame containing the name and the corresponding channel name in the aGDS file.} diff --git a/man/Gene_Centric_Noncoding_Results_Summary.Rd b/man/Gene_Centric_Noncoding_Results_Summary.Rd index c026438..1729dc5 100644 --- a/man/Gene_Centric_Noncoding_Results_Summary.Rd +++ b/man/Gene_Centric_Noncoding_Results_Summary.Rd @@ -20,8 +20,8 @@ Gene_Centric_Noncoding_Results_Summary( method_cond = c("optimal", "naive"), rare_maf_cutoff = 0.01, QC_label = "annotation/filter", - geno_missing_imputation = c("mean", "minor"), variant_type = c("SNV", "Indel", "variant"), + geno_missing_imputation = c("mean", "minor"), Annotation_dir = "annotation/info/FunctionalAnnotation", Annotation_name_catalog, Use_annotation_weights = FALSE, @@ -77,10 +77,10 @@ defining rare variants (default = 0.01).} \item{QC_label}{channel name of the QC label in the GDS/aGDS file (default = "annotation/filter").} -\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} - \item{variant_type}{type of variant included in the analysis. Choices include "SNV", "Indel", or "variant" (default = "SNV").} +\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} + \item{Annotation_dir}{channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation").} \item{Annotation_name_catalog}{a data frame containing the name and the corresponding channel name in the aGDS file.} diff --git a/man/Individual_Analysis_Results_Summary.Rd b/man/Individual_Analysis_Results_Summary.Rd index c41ad7e..da36943 100644 --- a/man/Individual_Analysis_Results_Summary.Rd +++ b/man/Individual_Analysis_Results_Summary.Rd @@ -14,6 +14,7 @@ Individual_Analysis_Results_Summary( known_loci = NULL, method_cond = c("optimal", "naive"), QC_label = "annotation/filter", + variant_type = c("variant", "SNV", "Indel"), geno_missing_imputation = c("mean", "minor"), alpha = 5e-09, manhattan_plot = FALSE, @@ -51,6 +52,8 @@ and taking the residuals (default = \code{optimal}).} \item{QC_label}{channel name of the QC label in the GDS/aGDS file.} +\item{variant_type}{type of variant included in the analysis. Choices include "variant", "SNV", or "Indel" (default = "variant").} + \item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} \item{alpha}{p-value threshold of significant results (default = 5E-09).} diff --git a/man/Sliding_Window_Results_Summary.Rd b/man/Sliding_Window_Results_Summary.Rd index e2780fe..01ce3e1 100644 --- a/man/Sliding_Window_Results_Summary.Rd +++ b/man/Sliding_Window_Results_Summary.Rd @@ -16,8 +16,8 @@ Sliding_Window_Results_Summary( method_cond = c("optimal", "naive"), rare_maf_cutoff = 0.01, QC_label = "annotation/filter", - geno_missing_imputation = c("mean", "minor"), variant_type = c("SNV", "Indel", "variant"), + geno_missing_imputation = c("mean", "minor"), Annotation_dir = "annotation/info/FunctionalAnnotation", Annotation_name_catalog, Use_annotation_weights = FALSE, @@ -64,10 +64,10 @@ defining rare variants (default = 0.01).} \item{QC_label}{channel name of the QC label in the GDS/aGDS file (default = "annotation/filter").} -\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} - \item{variant_type}{variants include in the conditional analysis. Choices include "variant", "SNV", or "Indel" (default = "SNV").} +\item{geno_missing_imputation}{method of handling missing genotypes. Either "mean" or "minor" (default = "mean").} + \item{Annotation_dir}{channel name of the annotations in the aGDS file \cr (default = "annotation/info/FunctionalAnnotation").} \item{Annotation_name_catalog}{a data frame containing the name and the corresponding channel name in the aGDS file.}