R/annotate_variants.R
subset_variant_by_type.Rd
Subsets a variant table based on Variant Type
subset_variant_by_type(tab, type)
tab | Input variant table |
---|---|
type | Variant type to return e.g. "SBS", "INS", "DEL", "DBS" |
Returns the input variant table subsetted to only contain variants of the specified variant type
#> chr start end ref alt sample #> 1: chr1 11020563 11020563 C A TCGA-94-7557-01A-11D-2122-08 #> 2: chr1 43430030 43430030 G T TCGA-94-7557-01A-11D-2122-08 #> 3: chr1 58682403 58682403 A G TCGA-94-7557-01A-11D-2122-08 #> 4: chr1 109508295 109508295 C G TCGA-94-7557-01A-11D-2122-08 #> 5: chr1 156384826 156384826 A C TCGA-94-7557-01A-11D-2122-08 #> --- #> 880: chr19 54885292 54885292 G A TCGA-ER-A19O-06A-11D-A197-08 #> 881: chr20 49374328 49374328 A T TCGA-ER-A19O-06A-11D-A197-08 #> 882: chrX 73213768 73213768 T G TCGA-ER-A19O-06A-11D-A197-08 #> 883: chrX 101292834 101292834 G A TCGA-ER-A19O-06A-11D-A197-08 #> 884: chrX 107526690 107526690 C T TCGA-ER-A19O-06A-11D-A197-08 #> Variant_Type #> 1: SBS #> 2: SBS #> 3: SBS #> 4: SBS #> 5: SBS #> --- #> 880: SBS #> 881: SBS #> 882: SBS #> 883: SBS #> 884: SBS