SIFTDbColumns

Description of the SIFT Sqlite Database Columns

classes

methods

Annotate variants, compute amino acid coding changes,
        predict coding outcomes.

Bioconductor Package Maintainer

VariantAnnotation

Annotation of Genetic Variants

SIFTDbColumns function

These column names are displayed when <code>columns</code> is called on a
  <code>SIFTDb</code> object.<p></p><p>    <ul><li>RSID : rsid</li><li>PROTEINID : NCBI RefSeq protein ID</li><li>AACHANGE : amino acid substitution; reference aa is preceeding,
                       followed by the position and finally the snp aa</li><li>METHOD : method of obtaining related sequences using PSI-BLAST</li><li>AA : either the reference or snp residue amino acid</li><li>PREDICTION : SIFT prediction</li><li>SCORE : SIFT score (range 0 to 1)<ul><li>TOLERATED : score is greater than 0.05</li><li>DAMAGING : score is less than or equal to 0.05</li><li>NOT SCORED : no prediction is made if there are less than 
                             2 homologous sequences that have an amino acid 
                             at the position of the given SNP or if the SIFT 
                             prediction is not available</li></ul></li><li>MEDIAN : diversity measurement of the sequences used for 
                     prediction (range 0 to 4.32)</li><li>POSITIONSEQS : number of sequences with an amino acide at the 
                           position of prediction</li><li>TOTALSEQS : total number of sequences in alignment</li></ul></p>

Column descriptions

These column names are displayed when <code>columns</code> is called on a
  <code>SIFTDb</code> object.

    <ul><li>RSID : rsid</li><li>PROTEINID : NCBI RefSeq protein ID</li><li>AACHANGE : amino acid substitution; reference aa is preceeding,
                       followed by the position and finally the snp aa</li><li>METHOD : method of obtaining related sequences using PSI-BLAST</li><li>AA : either the reference or snp residue amino acid</li><li>PREDICTION : SIFT prediction</li><li>SCORE : SIFT score (range 0 to 1)<ul><li>TOLERATED : score is greater than 0.05</li><li>DAMAGING : score is less than or equal to 0.05</li><li>NOT SCORED : no prediction is made if there are less than 
                             2 homologous sequences that have an amino acid 
                             at the position of the given SNP or if the SIFT 
                             prediction is not available</li></ul></li><li>MEDIAN : diversity measurement of the sequences used for 
                     prediction (range 0 to 4.32)</li><li>POSITIONSEQS : number of sequences with an amino acide at the 
                           position of prediction</li><li>TOTALSEQS : total number of sequences in alignment</li></ul>

SIFTDbColumns: SIFTDb Columns

Description

Arguments

Column descriptions

See Also