/usr/lib/R/site-library/VariantAnnotation/INDEX is in r-bioc-variantannotation 1.24.2-1.
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 34 35 | 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
indexVcf Create Index files for VCF file
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
seqinfo Get seqinfo for VCF file
snpSummary Counts and distribution statistics for SNPs in
a VCF object
summarizeVariants Summarize variants by sample
writeVcf Write VCF files
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