/usr/lib/R/site-library/VariantAnnotation/INDEX is in r-bioc-variantannotation 1.20.2-1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | GLtoGP Convert genotype likelihoods to genotype
probabilities
PROVEANDb-class PROVEANDb objects
PolyPhenDb-class PolyPhenDb objects
PolyPhenDbColumns PolyPhenDb Columns
SIFTDb-class SIFTDb objects
SIFTDbColumns SIFTDb Columns
ScanVcfParam-class Parameters for scanning VCF files
VCF-class VCF class objects
VCFHeader-class VCFHeader instances
VRanges-class VRanges objects
VRangesList-class VRangesList objects
VariantAnnotation-defunct
Defunct Functions in Package
'VariantAnnotation'
VariantType-class VariantType subclasses
VcfFile Manipulate Variant Call Format (Vcf) files.
filterVcf Filter VCF files
genotypeToSnpMatrix Convert genotype calls from a VCF file to a
SnpMatrix object
getTranscriptSeqs Get transcript sequences
isSNV Identification of genomic variant types.
locateVariants Locate variants
predictCoding Predict amino acid coding changes for variants
probabilityToSnpMatrix
Convert posterior genotype probability to a
SnpMatrix object
readVcf Read VCF files
scanVcf Import VCF files
snpSummary Counts and distribution statistics for SNPs in
a VCF object
summarizeVariants Summarize variants by sample
writeVcf Write VCF files
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