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STAARpipeline v0.9.8
STAARpipeline v0.9.8
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‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ Package: STAARpipeline
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Type: Package
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Title: STAARpipeline for Analyzing Whole-Genome/Whole-Exome Sequencing Data
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Version: 0.9.8
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Date: 2025-02-07
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Date: 2025-03-23
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Author: Xihao Li [aut, cre], Zilin Li [aut, cre], Wenbo Wang [aut], Sheila M. Gaynor [aut], Han Chen [aut]
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Maintainer: Xihao Li <xihaoli@unc.edu>, Zilin Li <lizl@nenu.edu.cn>, Wenbo Wang <wenbo@live.unc.edu>
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Description: An R package for performing STAARpipeline in analyzing whole-genome/whole-exome sequencing data.

‎R/coding.R‎

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@@ -659,9 +659,9 @@ coding <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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colnames(results_weight2)[i] <- c(i-1)
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}
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662-
results_weight_m <- results_weight; results_weight_ds <- c()
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results_weight1_m <- results_weight1; results_weight1_ds <- c()
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results_weight2_m <- results_weight2; results_weight2_ds <- c()
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results_weight_m <- results_weight
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results_weight1_m <- results_weight1
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results_weight2_m <- results_weight2
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rownames(pvalues_m$weight_all_1) <-rownames(pvalues_m$weight_all_2) <- unique(obj_nullmodel$pop.groups)
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@@ -671,18 +671,15 @@ coding <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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results_weight = results_weight_m,
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results_weight1 = results_weight1_m,
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results_weight2 = results_weight2_m)
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}
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}else
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{
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results_missense <- results
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results_ds <- c()
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results_missense <- c()
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results_ds <- results
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results <- c()
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results_weight_m <- results_weight_ds <- c()
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results_weight1_m <- results_weight1_ds <- c()
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results_weight2_m <- results_weight2_ds <- c()
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}
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}
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}
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if(!is.null(results))
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{
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if(dim(results)[1]==2)
@@ -710,7 +707,7 @@ coding <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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#results_weight
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if(use_ancestry_informed == TRUE & find_weight == TRUE){
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results_weight_m <- results_weight1_m <- results_weight2_m <- c()
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results_weight_m <- results_weight1_m <- results_weight2_m <- c()
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for(i in 1:ncol(pvalues_m$results_weight)){
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results_m_weight <- pvalues_m$results_weight[-c(1,2),i]

‎R/coding_incl_ptv.R‎

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Original file line numberDiff line numberDiff line change
@@ -894,9 +894,9 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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colnames(results_weight2)[i] <- c(i-1)
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}
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897-
results_weight_m <- results_weight; results_weight_ds <- c()
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results_weight1_m <- results_weight1; results_weight1_ds <- c()
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results_weight2_m <- results_weight2; results_weight2_ds <- c()
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results_weight_m <- results_weight
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results_weight1_m <- results_weight1
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results_weight2_m <- results_weight2
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rownames(pvalues_m$weight_all_1) <-rownames(pvalues_m$weight_all_2) <- unique(obj_nullmodel$pop.groups)
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@@ -906,18 +906,15 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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results_weight = results_weight_m,
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results_weight1 = results_weight1_m,
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results_weight2 = results_weight2_m)
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}
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}else
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{
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results_missense <- results
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results_ds <- c()
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results_missense <- c()
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results_ds <- results
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results <- c()
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results_weight_m <- results_weight_ds <- c()
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results_weight1_m <- results_weight1_ds <- c()
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results_weight2_m <- results_weight2_ds <- c()
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}
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}
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}
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if(!is.null(results))
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{
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if(dim(results)[1]==2)

‎R/missense.R‎

Lines changed: 29 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -402,7 +402,7 @@ missense <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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#results_weight
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if(use_ancestry_informed == TRUE & find_weight == TRUE){
405-
results_weight <- results_weight1 <- results_weight2 <- c()
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results_weight <- results_weight1 <- results_weight2 <- c()
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for(i in 1:ncol(pvalues$results_weight)){
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results_m_weight <- pvalues$results_weight[-c(1,2),i]
@@ -425,7 +425,7 @@ missense <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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colnames(results_weight)[i] <- c(i-1)
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}
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#results_weight1
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#results_weight1
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for(i in 1:ncol(pvalues$results_weight1)){
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results_m_weight1 <- pvalues$results_weight1[-c(1,2),i]
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results_m_weight1 <- unlist(pvalues$results_weight1[,i][c(5:length(pvalues$results_weight1[,i]), 4,3)])
@@ -447,35 +447,35 @@ missense <- function(chr,gene_name,genofile,obj_nullmodel,genes,
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colnames(results_weight1)[i] <- c(i-1)
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}
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450-
#results_weight2
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for(i in 1:ncol(pvalues$results_weight2)){
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results_m_weight2 <- pvalues$results_weight2[-c(1,2),i]
453-
results_m_weight2 <- unlist(pvalues$results_weight2[,i][c(5:length(pvalues$results_weight2[,i]), 4,3)])
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names(results_m_weight2) <- names(results_m)[-c(1:5,(length(results_m)-5):length(results_m))]
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results_m_weight2 <- c(results_m_weight2, rep(0,6))
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names(results_m_weight2)[(length(results_m_weight2)-5):length(results_m_weight2)] <- c("SKAT(1,25)-Disruptive","SKAT(1,1)-Disruptive","Burden(1,25)-Disruptive","Burden(1,1)-Disruptive","ACAT-V(1,25)-Disruptive","ACAT-V(1,1)-Disruptive")
458-
results_m_weight2[(length(results_m_weight2)-5):length(results_m_weight2)] <- unlist(pvalues_dm$results_weight2[,i][c("results_STAAR_S_1_25.SKAT(1,25)","results_STAAR_S_1_1.SKAT(1,1)","results_STAAR_B_1_25.Burden(1,25)",
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"results_STAAR_B_1_1.Burden(1,1)","results_STAAR_A_1_25.ACAT-V(1,25)","results_STAAR_A_1_1.ACAT-V(1,1)")])
460-
results_m_weight2["STAAR-O"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][p_seq]))
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results_m_weight2["STAAR-S(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num,6*apc_num+9)]))
462-
results_m_weight2["STAAR-S(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+(apc_num+1),6*apc_num+10)]))
463-
results_m_weight2["STAAR-B(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+2*(apc_num+1),6*apc_num+11)]))
464-
results_m_weight2["STAAR-B(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+3*(apc_num+1),6*apc_num+12)]))
465-
results_m_weight2["STAAR-A(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+4*(apc_num+1),6*apc_num+13)]))
466-
results_m_weight2["STAAR-A(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+5*(apc_num+1),6*apc_num+14)]))
450+
#results_weight2
451+
for(i in 1:ncol(pvalues$results_weight2)){
452+
results_m_weight2 <- pvalues$results_weight2[-c(1,2),i]
453+
results_m_weight2 <- unlist(pvalues$results_weight2[,i][c(5:length(pvalues$results_weight2[,i]), 4,3)])
454+
names(results_m_weight2) <- names(results_m)[-c(1:5,(length(results_m)-5):length(results_m))]
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468-
results_weight2 <- cbind(results_weight2, results_m_weight2)
469-
colnames(results_weight2)[i] <- c(i-1)
456+
results_m_weight2 <- c(results_m_weight2, rep(0,6))
457+
names(results_m_weight2)[(length(results_m_weight2)-5):length(results_m_weight2)] <- c("SKAT(1,25)-Disruptive","SKAT(1,1)-Disruptive","Burden(1,25)-Disruptive","Burden(1,1)-Disruptive","ACAT-V(1,25)-Disruptive","ACAT-V(1,1)-Disruptive")
458+
results_m_weight2[(length(results_m_weight2)-5):length(results_m_weight2)] <- unlist(pvalues_dm$results_weight2[,i][c("results_STAAR_S_1_25.SKAT(1,25)","results_STAAR_S_1_1.SKAT(1,1)","results_STAAR_B_1_25.Burden(1,25)",
459+
"results_STAAR_B_1_1.Burden(1,1)","results_STAAR_A_1_25.ACAT-V(1,25)","results_STAAR_A_1_1.ACAT-V(1,1)")])
460+
results_m_weight2["STAAR-O"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][p_seq]))
461+
results_m_weight2["STAAR-S(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num,6*apc_num+9)]))
462+
results_m_weight2["STAAR-S(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+(apc_num+1),6*apc_num+10)]))
463+
results_m_weight2["STAAR-B(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+2*(apc_num+1),6*apc_num+11)]))
464+
results_m_weight2["STAAR-B(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+3*(apc_num+1),6*apc_num+12)]))
465+
results_m_weight2["STAAR-A(1,25)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+4*(apc_num+1),6*apc_num+13)]))
466+
results_m_weight2["STAAR-A(1,1)"] <- CCT(as.numeric(results_m_weight2[1:length(results_m_weight2)][c(1:apc_num+5*(apc_num+1),6*apc_num+14)]))
467+
468+
results_weight2 <- cbind(results_weight2, results_m_weight2)
469+
colnames(results_weight2)[i] <- c(i-1)
470+
}
471+
rownames(pvalues$weight_all_1) <- rownames(pvalues$weight_all_2) <- unique(obj_nullmodel$pop.groups)
472+
results <- list(results,
473+
weight_all_1 = pvalues$weight_all_1,
474+
weight_all_2 = pvalues$weight_all_2,
475+
results_weight = results_weight,
476+
results_weight1 = results_weight1,
477+
results_weight2 = results_weight2)
470478
}
471-
rownames(pvalues$weight_all_1) <- rownames(pvalues$weight_all_2) <- unique(obj_nullmodel$pop.groups)
472-
results <- list(results,
473-
weight_all_1 = pvalues$weight_all_1,
474-
weight_all_2 = pvalues$weight_all_2,
475-
results_weight = results_weight,
476-
results_weight1 = results_weight1,
477-
results_weight2 = results_weight2)
478-
}
479479
}else
480480
{
481481
results_m <- c(results[1,],rep(0,2))

‎README.md‎

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@@ -31,7 +31,7 @@ Please see the <a href="docs/STAARpipeline_manual.pdf">**STAARpipeline** user ma
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## Data Availability
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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).
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## Version
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The current version is 0.9.8 (February 7, 2025).
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The current version is 0.9.8 (March 23, 2025).
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## Citation
3636
If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite:
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