STAARpipeline v0.9.7

xihaoli · Mar 27, 2024 · 08375b6 · 08375b6
1 parent 6a66553
commit 08375b6
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Showing 3 changed files with 2 additions and 8 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -13,7 +13,7 @@ jobs:
         run: |
           brew install imagemagick@6
           brew install libgit2
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: 4.2.3
@@ -30,6 +30,7 @@ jobs:
           needs: |
             website
             coverage
+          install-pandoc: true
       - name: Check
         run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
         shell: Rscript {0}
diff --git a/R/coding.R b/R/coding.R
@@ -213,7 +213,6 @@ coding <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 	#####################################################
 	#                      plof
 	#####################################################
-	# variant.id.gene <- seqGetData(genofile, "variant.id")
 	lof.in.plof <- (GENCODE.EXONIC.Category=="stopgain")|(GENCODE.EXONIC.Category=="stoploss")|(GENCODE.Category=="splicing")|(GENCODE.Category=="exonic;splicing")|(GENCODE.Category=="ncRNA_splicing")|(GENCODE.Category=="ncRNA_exonic;splicing")
 	variant.id.gene.category <- variant.id.gene[lof.in.plof]
 

diff --git a/R/coding_incl_ptv.R b/R/coding_incl_ptv.R
@@ -210,7 +210,6 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 		}
 	}
 
-
 	################################################
 	#                  ptv_ds
 	################################################
@@ -323,7 +322,6 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 	#####################################################
 	#                      plof
 	#####################################################
-	# variant.id.gene <- seqGetData(genofile, "variant.id")
 	lof.in.plof <- (GENCODE.EXONIC.Category=="stopgain")|(GENCODE.EXONIC.Category=="stoploss")|(GENCODE.Category=="splicing")|(GENCODE.Category=="exonic;splicing")|(GENCODE.Category=="ncRNA_splicing")|(GENCODE.Category=="ncRNA_exonic;splicing")
 	variant.id.gene.category <- variant.id.gene[lof.in.plof]
 
@@ -413,12 +411,9 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 		}
 	}
 
-
 	#####################################################
 	#                      ptv
 	#####################################################
-	# variant.id.gene <- seqGetData(genofile, "variant.id")
-
 	if(variant_type=="SNV")
 	{
 		lof.in.plof <- (GENCODE.EXONIC.Category=="stopgain")|(GENCODE.EXONIC.Category=="stoploss")|(GENCODE.Category=="splicing")|(GENCODE.Category=="exonic;splicing")
@@ -524,7 +519,6 @@ coding_incl_ptv <- function(chr,gene_name,genofile,obj_nullmodel,genes,
 		}
 	}
 
-
 	#############################################
 	#             synonymous
 	#############################################