CollapsedVCF object, read in with the readVcf function
from the VariantAnnotation package.
tumor.id.in.vcf
The tumor id in the CollapsedVCF (optional).
use.somatic.status
If somatic status and germline data is available, then use this
information to remove non-heterozygous germline SNPs or germline SNPS
with biased allelic fractions.
snp.blacklist
CSV file with SNP ids with expected allelic fraction
significantly different from 0.5 in diploid genomes. Can be an array of
lists. The function createSNPBlacklist can provide appropriate black
lists.
af.range
Exclude SNPs with allelic fraction smaller or greater than the
two values, respectively.
contamination.cutoff
Count SNPs in dbSNP with allelic fraction smaller than the
first value, if found on most chromosomes, remove all with AF smaller than
the second value.
coverage.cutoff
Minimum coverage in tumor. Variants with lower coverage are ignored.
min.supporting.reads
Minimum number of reads supporting the alt allele.
verbose
Value
A list with elements
vcf
The filtered CollapsedVCF object.
flag
A flag (TRUE/FALSE) if problems were identified.
flag_comment
A comment describing the flagging.
Author(s)
Markus Riester
Examples
# This function is typically only called by runAbsolute via the
# fun.filterVcf and args.filterVcf comments.
library(VariantAnnotation)
vcf.file <- system.file("extdata", "example_vcf.vcf", package="PureCN")
vcf <- readVcf(vcf.file, "hg19")
vcf.filtered <- filterVcfBasic(vcf)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PureCN/filterVcfBasic.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterVcfBasic
> ### Title: Basic VCF filter function
> ### Aliases: filterVcfBasic
>
> ### ** Examples
>
> # This function is typically only called by runAbsolute via the
> # fun.filterVcf and args.filterVcf comments.
> library(VariantAnnotation)
> vcf.file <- system.file("extdata", "example_vcf.vcf", package="PureCN")
> vcf <- readVcf(vcf.file, "hg19")
> vcf.filtered <- filterVcfBasic(vcf)
Removing 0 non heterozygous (in matched normal) germline SNPs.
Removing 108 SNPs with AF < 0.03 or AF >= 0.97 or less than 3 supporting reads or depth < 20.
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.