The PolyPhenDb class is a container for storing a connection to a PolyPhen sqlite database.
PolyPhen (Polymorphism Phenotyping) is a tool which predicts the possible impact of an amino acid substitution on the structure and function of a human protein by applying empirical rules to the sequence, phylogenetic and structural information characterizing the substitution.
PolyPhen makes its predictions using UniProt features, PSIC profiles scores derived from multiple alignment and matches to PDP or PQS structural databases. The procedure can be roughly outlined in the following steps, see the references for complete details,
sequence-based characterization of substitution site
calculation of PSIC profile scores for two amino acid variants
calculation of structural parameters and contacts
PolyPhen uses empirically derived rules to predict that a non-synonymous SNP is
probably damaging : it is with high confidence supposed to affect protein function or structure
possibly damaging : it is supposed to affect protein function or structure
benign : most likely lacking any phenotypic effect
unknown : when in some rare cases, the lack of data do not allow PolyPhen to make a prediction
In the code below,
x is a
x's metadata in a data frame.
Returns the names of the
columns that can be used to subset the
data columns. For column descriptions see
Returns the names of the
keys that can be used to subset the
data rows. The
keys values are the rsid's.
select(x, keys = NULL, columns = NULL, ...):
Returns a subset of data defined by the character vectors
columns. If no
keys are supplied, all rows are
returned. If no
columns are supplied, all columns
are returned. See
?PolyPhenDbColumns for column descriptions.
Returns a named list of duplicate rsid groups. The names are the
keys, the list elements are the rsid's that have been
reported as having identical chromosome position and alleles and
therefore translating into the same amino acid residue substitution.
PolyPhen Home: http://genetics.bwh.harvard.edu/pph2/dokuwiki/
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. Nat Methods 7(4):248-249 (2010).
Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30(17):3894-3900 (2002).
Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng 12(5):387-394 (1999).
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library(PolyPhen.Hsapiens.dbSNP131) ## metadata metadata(PolyPhen.Hsapiens.dbSNP131) ## available rsid's head(keys(PolyPhen.Hsapiens.dbSNP131)) ## column descriptions found at ?PolyPhenDbColumns columns(PolyPhen.Hsapiens.dbSNP131) ## subset on keys and columns subst <- c("AA1", "AA2", "PREDICTION") rsids <- c("rs2142947", "rs4995127", "rs3026284") select(PolyPhen.Hsapiens.dbSNP131, keys=rsids, columns=subst) ## retrieve substitution scores subst <- c("IDPMAX", "IDPSNP", "IDQMIN") select(PolyPhen.Hsapiens.dbSNP131, keys=rsids, columns=subst) ## retrieve the PolyPhen-2 classifiers subst <- c("PPH2CLASS", "PPH2PROB", "PPH2FPR", "PPH2TPR", "PPH2FDR") select(PolyPhen.Hsapiens.dbSNP131, keys=rsids, columns=subst) ## duplicate groups of rsid's duplicateRSID(PolyPhen.Hsapiens.dbSNP131, c("rs71225486", "rs1063796"))
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