SnpAnnotationSQLite-class: Class SnpAnotationSQLite

Description Constructor Accessors Author(s) See Also Examples

Description

The SnpAnnotationSQLite class stores annotation data associated with SNPs, as well as metadata describing each column, in an SQLite database.

Constructor

SnpAnnotationSQLite(dbpath):

dbpath is the path to a SQLite database with tables "Annotation" and "Metadata." "Annotation" must contain at least the following columns:

  • "snpID": integer vector containing unique SNP ids.

  • "chromosome": integer vector containing chromosome codes.

  • "position": integer vector containing position (in base pairs) on the chromosome.

Default values for chromosome codes are 1-22=autosome, 23=X, 24=XY, 25=Y, 26=M. The defaults may be changed with the arguments autosomeCode, XchromCode, XYchromCode, YchromCode, and MchromCode.

"Metadata" must contain at least the following columns:

  • "varname": name of variable in annotation

  • "description": description of column in annotation

If the database does not yet exist, a database is created with tables "Annotation" and "Metadata."

The SnpAnnotationSQLite constructor creates and returns a SnpAnnotationSQLite instance.

Accessors

In the code snippets below, object is a SnpAnnotationSQLite object.

open(object): Opens a connection to the database.

close(object): Closes the database connection.

nsnp(object): The number of SNPs in the database.

getSnpID(object, index, condition): A unique integer vector of snp IDs. The optional index is a logical or integer vector specifying elements to extract. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1").

getChromosome(object, index, condition, char=FALSE): A vector of chromosomes. The optional index is a logical or integer vector specifying elements to extract. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1"). If char=FALSE (default), returns an integer vector. If char=TRUE, returns a character vector with elements in (1:22,X,XY,Y,M,U). "U" stands for "Unknown" and is the value given to any chromosome code not falling in the other categories.

getPosition(object, index, condition): An integer vector of base pair positions. The optional index is a logical or integer vector specifying elements to extract. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1").

getAlleleA(object, index): A character vector of A alleles. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1").

getAlleleB(object, index): A character vector of B alleles. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1").

getVariable(object, varname, index, condition): A vector of the column varname. The optional index is a logical or integer vector specifying elements to extract. The optional condition is a character string with an SQL clause used to select data (e.g., "LIMIT 10", "WHERE chromosome=1"). Returns NULL if varname is not found in object.

hasVariable(object, varname): Returns TRUE if varname is a column in object, FALSE if not.

getVariableNames(object): Returns a character vector with the names of all columns in object.

getAnnotation(object): Returns all annotation variables as a data frame.

getMetadata(object): Returns metadata describing the annotation variables as a data frame.

getQuery(object, statement): Returns result of the SQL query statement.

writeAnnotation(object, value, append=FALSE, overwrite=TRUE): Writes value to the SNP annotation table. value must be a data.frame containing columns "snpID", "chromosome", and "position".

writeMetadata(object, value, append=FALSE, overwrite=TRUE): Writes value to the metadata table. value should be a data.frame containing columns "varname" and "description".

autosomeCode(object): Returns the integer codes for the autosomes.

XchromCode(object): Returns the integer code for the X chromosome.

XYchromCode(object): Returns the integer code for the pseudoautosomal region.

YchromCode(object): Returns the integer code for the Y chromosome.

MchromCode(object): Returns the integer code for mitochondrial SNPs.

Author(s)

Stephanie Gogarten

See Also

ScanAnnotationSQLite, SnpAnnotationDataFrame, GenotypeData, IntensityData

Examples

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library(GWASdata)
dbpath <- tempfile()
snpAnnot <- SnpAnnotationSQLite(dbpath)

data(illumina_snp_annot)
writeAnnotation(snpAnnot, illumina_snp_annot)

# list columns
vars <- getVariableNames(snpAnnot)

# add metadata
metadf <- data.frame(varname=vars, description=rep(NA, length(vars)),
  row.names=vars, stringsAsFactors=FALSE)
metadf["snpID", "description"] <- "integer id"
writeMetadata(snpAnnot, metadf)

# get snpID and chromosome
snpID <- getSnpID(snpAnnot)
chrom <- getChromosome(snpAnnot)

# get positions only for chromosome 22
pos22 <- getPosition(snpAnnot, condition="WHERE chromosome = 22")

# get rsID
if (hasVariable(snpAnnot, "rsID")) rsID <- getVariable(snpAnnot, "rsID")

# display data
head(getAnnotation(snpAnnot))
getMetadata(snpAnnot)

close(snpAnnot)
file.remove(dbpath)

amstilp/GWASTools documentation built on May 10, 2019, 1:08 a.m.