STAARpipeline

xihaoli · Feb 17, 2024 · e10b878 · e10b878
1 parent e2e87fe
commit e10b878
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Showing 8 changed files with 16 additions and 16 deletions.
diff --git a/STAARpipeline_Dynamic_Window.r b/STAARpipeline_Dynamic_Window.r
@@ -2,7 +2,7 @@
 # Dynamic window analysis using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 12/28/2022
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -48,7 +48,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_SCANG"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Gene_Centric_Coding.r b/STAARpipeline_Gene_Centric_Coding.r
@@ -2,7 +2,7 @@
 # Gene-centric analysis for coding rare variants using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 12/28/2022
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -45,7 +45,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Coding"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Gene_Centric_Coding_Long_Masks.r b/STAARpipeline_Gene_Centric_Coding_Long_Masks.r
@@ -2,7 +2,7 @@
 # Gene-centric analysis for coding rare variants in long masks using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 02/05/2024
+# Current date: 02/16/2024
 ##################################################################################
 rm(list=ls())
 gc()
@@ -45,7 +45,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Coding"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid_longmask <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Gene_Centric_Noncoding.r b/STAARpipeline_Gene_Centric_Noncoding.r
@@ -3,7 +3,7 @@
 # genes using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 02/05/2024
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -46,7 +46,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Noncoding"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r b/STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r
@@ -3,7 +3,7 @@
 # of protein-coding genes using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 02/05/2024
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -46,7 +46,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Noncoding"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid_longmask <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Gene_Centric_ncRNA.r b/STAARpipeline_Gene_Centric_ncRNA.r
@@ -3,7 +3,7 @@
 # genes using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 02/05/2024
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -46,7 +46,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_ncRNA"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Individual_Analysis.r b/STAARpipeline_Individual_Analysis.r
@@ -2,7 +2,7 @@
 # Individual analysis using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 12/28/2022
+# Current date: 02/16/2024
 ###########################################################
 rm(list=ls())
 gc()
@@ -35,7 +35,7 @@ geno_missing_imputation <- "mean"
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Individual_Analysis"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################

diff --git a/STAARpipeline_Sliding_Window.r b/STAARpipeline_Sliding_Window.r
@@ -2,7 +2,7 @@
 # Sliding window analysis using STAARpipeline
 # Xihao Li, Zilin Li
 # Initiate date: 11/04/2021
-# Current date: 12/28/2022
+# Current date: 02/16/2024
 #####################################################################
 rm(list=ls())
 gc()
@@ -49,7 +49,7 @@ Annotation_name <- c("CADD","LINSIGHT","FATHMM.XF","aPC.EpigeneticActive","aPC.E
 output_path <- "/path_to_the_output_file/"
 ## output file name
 output_file_name <- "TOPMed_F5_LDL_Sliding_Window"
-## input array id from batch file (Harvard FAS RC cluster)
+## input array id from batch file
 arrayid <- as.numeric(commandArgs(TRUE)[1])
 
 ###########################################################