STAARpipelineSummary v0.9.6

xihaoli · Apr 16, 2022 · 3fafd16 · 3fafd16
2 parents 3c957ef + a4d745a
commit 3fafd16
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: STAARpipelineSummary
 Type: Package
 Title: Summarization and Visualization of Analysis Results Generated by STAARpipeline
 Version: 0.9.6
-Date: 2022-02-17
+Date: 2022-04-16
 Author: Xihao Li [aut, cre], Zilin Li [aut, cre]
 Maintainer: Xihao Li <xihaoli@g.harvard.edu>, Zilin Li <li@hsph.harvard.edu>
 Description: An R package for summarizing analysis results generated by STAARpipeline.

diff --git a/R/Annotate_Single_Variants.R b/R/Annotate_Single_Variants.R
@@ -1,4 +1,4 @@
-#' Functionally annotate a list of variants.
+#' Functionally annotate a list of variants
 #'
 #' The \code{Annotate_Single_Variants} function takes in a list of variants to functionally annotate the input variants
 #' @param agds_dir file directory of annotated GDS (aGDS) files for all chromosomes (1-22).
@@ -7,14 +7,14 @@
 #' @param QC_label channel name of the QC label in the GDS/aGDS file  (default = "annotation/filter").
 #' @param Annotation_dir channel name of the annotations in the aGDS file (default = "annotation/info/FunctionalAnnotation").
 #' @param Annotation_name_catalog a data frame containing the annotation names and the corresponding channel names in the aGDS file.
-#' @param Annotation_name a vector of annotation names used in STAAR (default = NULL).
+#' @param Annotation_name a vector of qualitative/quantitative annotation names user wants to extract.
 #' @return a data frame containing the basic information (chromosome, position, reference allele and alternative allele)
 #' and annotation scores for the input variants.
 #' @export
 
 Annotate_Single_Variants <- function(agds_dir,single_variants_list,
                                      QC_label="annotation/filter",Annotation_dir="annotation/info/FunctionalAnnotation",
-                                     Annotation_name_catalog,Annotation_name=NULL){
+                                     Annotation_name_catalog,Annotation_name){
 
 	single_variants_list_info <- single_variants_list[,c("CHR","POS","REF","ALT")]
 
@@ -76,5 +76,3 @@ Annotate_Single_Variants <- function(agds_dir,single_variants_list,
 	return(single_variants_list_info_annotation)
 }
 
-
-
diff --git a/R/Dynamic_Window_Results_Summary.R b/R/Dynamic_Window_Results_Summary.R
@@ -1,5 +1,5 @@
 #' Summarize the results of dynamic window analysis generated by \code{STAARpipeline} package and
-#' perform conditional analysis for (unconditionally) significant genetic regions by adjusting for a given list of known variants.
+#' perform conditional analysis for (unconditionally) significant genetic regions by adjusting for a given list of known variants
 #'
 #' The \code{Dynamic_Window_Results_Summary} function takes in the results of dynamic window analysis generated by \code{STAARpipeline} package,
 #' the object from fitting the null model, and the set of known variants to be adjusted for in conditional analysis
@@ -171,7 +171,7 @@ Dynamic_Window_Results_Summary <- function(agds_dir,jobs_num,input_path,output_p
 	emthr_genome <- apply(SCANG_B_emthr,2,max)
 
 	thr <- quantile(emthr_genome,1-alpha)
-	SCANG_B_res <- SCANG_B_res[SCANG_B_res[,1]>thr,]
+	SCANG_B_res <- SCANG_B_res[SCANG_B_res[,1]>thr,,drop=FALSE]
 
 	if(length(SCANG_B_res)>=6)
 	{

diff --git a/R/Gene_Centric_Coding_Info.R b/R/Gene_Centric_Coding_Info.R
@@ -23,7 +23,7 @@
 #' @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 (default = "annotation/info/FunctionalAnnotation").
 #' @param Annotation_name_catalog a data frame containing the name and the corresponding channel name in the aGDS file.
-#' @param Annotation_name a vector of annotation names used in STAAR (default = NULL).
+#' @param Annotation_name a vector of qualitative/quantitative annotation names user wants to extract.
 #' @return a data frame containing the basic information (chromosome, position, reference allele and alternative allele),
 #' unconditional and conditional the score test p-values,
 #' and annotation scores for the rare variants of the input coding mask.
@@ -33,7 +33,7 @@ Gene_Centric_Coding_Info <- function(category=c("plof","plof_ds","missense","dis
                                      chr,genofile,obj_nullmodel,gene_name,known_loci=NULL,rare_maf_cutoff=0.01,
                                      method_cond=c("optimal","naive"),
                                      QC_label="annotation/filter",variant_type=c("SNV","Indel","variant"),geno_missing_imputation=c("mean","minor"),
-                                     Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog,Annotation_name=NULL){
+                                     Annotation_dir="annotation/info/FunctionalAnnotation",Annotation_name_catalog,Annotation_name){
 
 	## evaluate choices
 	category <- match.arg(category)