# Genomewide Epistasis Analysis on Bacteria

## Documentation for package ‘LDWeaver’ version 1.5.1

- DESCRIPTION file.

## Help Pages

.mat | .mat
.rescale01 | .rescale01
._legendfun2 | ._legendfun2
analyse_long_range_links | analyse_long_range_links
cleanup | cleanup
cleanup_support | cleanup_support
create_network | create_network
create_network_for_gene | create_network_for_gene
create_tanglegram | create_tanglegram
estimate_Hamming_distance_weights | estimate_Hamming_distance_weights
estimate_variation_in_CDS | estimate_variation_in_CDS
GBAccession | GBAccession ID class
GBAccession-class | GBAccession ID class
GBFile-class | GenBank File
GBKFile-class | GenBank File
GenBankFile-class | GenBank File
GenBankRecord-class | GenBank data objects.
generate_Links_SNPS_fasta | generate_Links_SNPS_fasta
genomewide_LDMap | genomewide_LDMap
LDWeaver | LDWeaver
make_gwes_plots | make_gwes_plots
parse_fasta_alignment | extractSNP_from_MSA
parse_fasta_SNP_alignment | extractSNPs_from_SNP_MSA
parse_genbank_file | parse_genbank_file
parse_gff_file | parse_gff_file
perform_MI_computation | perform_MI_computation
perform_snpEff_annotations | perform_snpEff_annotations
read_AnnotatedLinks | read_AnnotatedLinks
read_GFF3_Annotation | read_GFF3_Annotation
read_LongRangeLinks | read_LongRangeLinks
read_ReferenceFasta | read_ReferenceFasta
read_ShortRangeLinks | read_ShortRangeLinks
read_TopHits | read_TopHits
runARACNE | runARACNE
snpdat_to_fa | snpdat_to_fa
view_tree | view_tree
write_output_for_gwes_explorer | write_output_for_gwes_explorer