STAARpipelineSummary v0.9.7

xihaoli · xihaoli · commit 553cb216cc11 · 2024-07-25T22:54:26.000-04:00
diff --git a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
@@ -189,7 +189,6 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 	# ptv + disruptive missense
 	results_ptv_ds_genome <- results_ptv_ds_genome[results_ptv_ds_genome[,"cMAC"]>cMAC_cutoff,]
 
-
 	### recalculate missense pvalue
 	if(cMAC_cutoff > 0)
 	{
@@ -342,7 +341,6 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 		}
 	}
 
-
 	###### whole-genome results
 	# plof
 	save(results_plof_genome,file=paste0(output_path,"plof.Rdata"))

Original file line number	Diff line number	Diff line change
`@@ -189,7 +189,6 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c`
`189`	`189`	`# ptv + disruptive missense`
`190`	`190`	`results_ptv_ds_genome <- results_ptv_ds_genome[results_ptv_ds_genome[,"cMAC"]>cMAC_cutoff,]`
`191`	`191`
`192`		`-`
`193`	`192`	`### recalculate missense pvalue`
`194`	`193`	`if(cMAC_cutoff > 0)`
`195`	`194`	`{`
`@@ -342,7 +341,6 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c`
`342`	`341`	`}`
`343`	`342`	`}`
`344`	`343`
`345`		`-`
`346`	`344`	`###### whole-genome results`
`347`	`345`	`# plof`
`348`	`346`	`save(results_plof_genome,file=paste0(output_path,"plof.Rdata"))`