From e10b8783d43a9bee61c805e7fd0da11376461222 Mon Sep 17 00:00:00 2001 From: Xihao Li Date: Fri, 16 Feb 2024 21:07:39 -0500 Subject: [PATCH] STAARpipeline --- STAARpipeline_Dynamic_Window.r | 4 ++-- STAARpipeline_Gene_Centric_Coding.r | 4 ++-- STAARpipeline_Gene_Centric_Coding_Long_Masks.r | 4 ++-- STAARpipeline_Gene_Centric_Noncoding.r | 4 ++-- STAARpipeline_Gene_Centric_Noncoding_Long_Masks.r | 4 ++-- STAARpipeline_Gene_Centric_ncRNA.r | 4 ++-- STAARpipeline_Individual_Analysis.r | 4 ++-- STAARpipeline_Sliding_Window.r | 4 ++-- 8 files changed, 16 insertions(+), 16 deletions(-) diff --git a/STAARpipeline_Dynamic_Window.r b/STAARpipeline_Dynamic_Window.r index fed1bcd..1151c77 100644 --- 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 index b277244..9f6e5cb 100644 --- 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 index 20968da..2b4de50 100644 --- 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 index ccbddec..06949e5 100644 --- 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 index ca8a488..f16036c 100644 --- 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 index 446ae7d..afa803b 100644 --- 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 index 842552d..c6794b1 100644 --- 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 index 6d7ba0e..4fe06b1 100644 --- 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]) ###########################################################