Description Usage Arguments Examples
View source: R/vcf_to_mutations_df.R
Uses VariantAnnotation::readVcfAsVRanges to read the vcf file, which return variants in a format that each row is one variant. If the vcf has multiple samples, the samples will be appended by rows. Provide a sample_name to return only the variants belonging to the sample of interest. Once you use this function, make sure that all the variants are relevant. The function will only return SNVs.
1 | vcf_to_mutations_df(vcf, sample_name = NULL, ...)
|
vcf |
the path to vcf file |
sample_name |
a character(1) when provided, return only variants from this sample |
... |
other options passed to VariantAnnotation::readVcfAsVRanges |
1 2 | vcf <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf_to_mutations_df(vcf, sample_name = "HG00096")
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