PROVEANDb-class {VariantAnnotation} | R Documentation

## PROVEANDb objects

### Description

The PROVEANDb class is a container for storing a connection to a PROVEAN sqlite database.

### Details

The SIFT tool is no longer actively maintained. A few of the orginal authors have started the PROVEAN (Protein Variation Effect Analyzer) project. PROVEAN is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important.

See the web pages for a complete description of the methods.

- PROVEAN Home: http://provean.jcvi.org/index.php/

- SIFT Home: http://sift.jcvi.org/

Though SIFT is not under active development, the PROVEAN team still provids the SIFT scores in the pre-computed downloads. This package, `SIFT.Hsapiens.dbSNP137`, contains both SIFT and PROVEAN scores. One notable difference between this and the previous SIFT database package is that `keys` in `SIFT.Hsapiens.dbSNP132` are rs IDs whereas in `SIFT.Hsapiens.dbSNP137` they are NCBI dbSNP IDs.

### Methods

In the code below, `x` is a `PROVEANDb` object.

  `metadata(x)`: Returns `x`'s metadata in a data frame.

  `columns(x)`: Returns the names of the `columns` that can be used to subset the data columns.

  `keys(x, keytype="DBSNPID", ...)`: Returns the names of the `keys` that can be used to subset the data rows. For SIFT.Hsapiens.dbSNP137 the `keys` are NCBI dbSNP ids.

  `keytypes(x)`: Returns the names of the `columns` that can be used as `keys`. For SIFT.Hsapiens.dbSNP137 the NCBI dbSNP ids are the only keytype.

  `select(x, keys = NULL, columns = NULL, keytype = "DBSNPID", ...)`: Returns a subset of data defined by the character vectors `keys` and `columns`. If no `keys` are supplied, all rows are returned. If no `columns` are supplied, all columns are returned.

### Author(s)

Valerie Obenchain

### References

The PROVEAN tool has replaced SIFT: http://provean.jcvi.org/about.php

Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the Functional Effect of Amino Acid Substitutions and Indels. PLoS ONE 7(10): e46688.

Choi Y (2012) A Fast Computation of Pairwise Sequence Alignment Scores Between a Protein and a Set of Single-Locus Variants of Another Protein. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB '12). ACM, New York, NY, USA, 414-417.

Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81

Ng PC, Henikoff S. Predicting the Effects of Amino Acid Substitutions on Protein Function Annu Rev Genomics Hum Genet. 2006;7:61-80.

Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4.

### Examples

      if (require(SIFT.Hsapiens.dbSNP137)) {
          ## metadata
          metadata(SIFT.Hsapiens.dbSNP137)

          ## keys are the DBSNPID (NCBI dbSNP ID)
          dbsnp <- keys(SIFT.Hsapiens.dbSNP137)
          head(dbsnp)
          columns(SIFT.Hsapiens.dbSNP137)

          ## Return all columns. Note that the key, DBSNPID,
          ## is always returned.
          select(SIFT.Hsapiens.dbSNP137, dbsnp[10])
          ## subset on keys and cols
          cols <- c("VARIANT", "PROVEANPRED", "SIFTPRED")
          select(SIFT.Hsapiens.dbSNP137, dbsnp[20:23], cols)
      }

[Package VariantAnnotation version 1.34.0 Index]