STAARpipeline v0.9.7

xihaoli · Jun 26, 2024 · 94b5d2b · 94b5d2b
1 parent d29febc
commit 94b5d2b
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/R/coding.R b/R/coding.R
@@ -627,7 +627,7 @@ coding <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 						results_m[length(results_m)] <- 1
 					}
 
-					apc_num <- (length(results_m)-10)/6
+					apc_num <- (length(results_m)-10)/2
 					p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),(length(results_m)-6):(length(results_m)-5))
 
 					## calculate STAAR-B

diff --git a/R/coding_incl_ptv.R b/R/coding_incl_ptv.R
@@ -844,7 +844,7 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 						results_m[length(results_m)] <- 1
 					}
 
-					apc_num <- (length(results_m)-10)/6
+					apc_num <- (length(results_m)-10)/2
 					p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),(length(results_m)-6):(length(results_m)-5))
 
 					## calculate STAAR-B

diff --git a/R/missense.R b/R/missense.R
@@ -356,7 +356,7 @@ missense <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 						results_m[length(results_m)] <- 1
 					}
 
-					apc_num <- (length(results_m)-10)/6
+					apc_num <- (length(results_m)-10)/2
 					p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),(length(results_m)-6):(length(results_m)-5))
 
 					## calculate STAAR-B

diff --git a/R/missense_cond_spa.R b/R/missense_cond_spa.R
@@ -328,7 +328,7 @@ missense_cond_spa <- function(chr,gene_name,genofile,obj_nullmodel,genes,known_l
 					results_m[length(results_m)] <- 1
 				}
 
-				apc_num <- (length(results_m)-10)/6
+				apc_num <- (length(results_m)-10)/2
 				p_seq <- c(1:apc_num,1:apc_num+(apc_num+1),(length(results_m)-6):(length(results_m)-5))
 
 				## calculate STAAR-B