applyFilters.Rd
This function calls the callFilters() function on each element of a list of CollapsedVCF objects and generates in output a list of lists. Each list corresponds to one input element, and consists in four elements: an object containg variants which passed the filter, a character string describing the applied filter (if any), an object containing the sequencing design and a character string with the name of the sample.
applyFilters( vcfs, assembly, design, vaf.cutoff = 0, remove.nonexonic = TRUE, remove.cancer = FALSE, tsList = NULL, variantType = c() )
vcfs | a |
---|---|
assembly | human genome assembly: hg19 or hg38 |
design | a |
vaf.cutoff | minimum value of variant allele frequency accepted |
remove.nonexonic | logical value 'TRUE' or 'FALSE' indicating whether or not SNV mapped ouside of exons are to be removed. Default is True |
remove.cancer | logical value 'TRUE' or 'FALSE' indicating whether or not to remove cancer variants (variants described in COSMIC and truncating mutations in tumor suppressors) |
tsList | path to file containing list of tumor suppressors. If not provided a list of 1217 tumor suppressors from the TSgene2 database (<http://bioinfo.mc.vanderbilt.edu/TSGene/>) is used by default. |
variantType | type of variant to remove. Possible values: synonymous,
nonsynonymous, frameshift, nonsense, not translated or a combination of them
specified in a |
Returns a list
of lists
. Each list
include the
following elements: a GRanges
, CollapsedVCF
, data.frame
object containing variants passing the filter, a charcater string
describing applied filter (if any), a GRanges
or character vector
with the sequencing design, a character string
with the name of the
sample.
Laura Fancello
## Read vcf vcf_files <- list(Horizon5="Horizon5_ExamplePanel.vcf", HorizonFFPEmild="HorizonFFPEmild_ExamplePanel.vcf") vcf_files <- lapply(vcf_files , function(x) system.file("extdata", x, package = "TMBleR", mustWork = TRUE)) vcfs <- readVcfFiles(vcfFiles = vcf_files, assembly = "hg19")#>#> $Horizon5 #> $Horizon5$warnings #> [1] "line 141: The VCF file contains 2 samples. Only the first (1_20170317_01_i01_0_horizon_5) will be used" #> [2] "line 142: AF is described both in FORMAT and in INFO of this and possibly other variants. FORMAT's AF will be used" #> #> $Horizon5$errors #> NULL #> #> #> $HorizonFFPEmild #> $HorizonFFPEmild$warnings #> [1] "line 141: The VCF file contains 2 samples. Only the first (2_20170317_01_i01_0_horizon_ffpe_mild) will be used" #> [2] "line 142: AF is described both in FORMAT and in INFO of this and possibly other variants. FORMAT's AF will be used" #> #> $HorizonFFPEmild$errors #> NULL #> #>#>#> Warning: replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’## Read design design <- readDesign(system.file("extdata" , "ExamplePanel_GeneIDs.txt" , package = "TMBleR" , mustWork = TRUE) , assembly = "hg19" , ids = "entrezgene_id")#> Warning: `select_()` is deprecated as of dplyr 0.7.0. #> Please use `select()` instead. #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_warnings()` to see where this warning was generated.#> Warning: `filter_()` is deprecated as of dplyr 0.7.0. #> Please use `filter()` instead. #> See vignette('programming') for more help #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_warnings()` to see where this warning was generated.#>## Apply filter to remove known cancer variants using the default tumor ## suppressors list vcfs_NoCancer <- applyFilters(vcfs = vcfs , assembly = "hg19" , design = design , remove.cancer = TRUE , tsList = NULL , variantType = NULL)#> Warning: data object COSMIC_hg19 was not found. Loading a COSMIC demo dataset. Please do not use this for TMB analysis but only for demoing TMBleR#> Warning: data object COSMIC_hg19 was not found. Loading a COSMIC demo dataset. Please do not use this for TMB analysis but only for demoing TMBleR## Apply filter to remove synonymous mutations vcfs_filtered <- applyFilters(vcfs = vcfs, assembly = "hg19", design = design, remove.cancer = FALSE, tsList = NULL, variantType = "synonymous")