SnpAnnotationSQLite-class: Class SnpAnotationSQLite

In amstilp/GWASTools: Tools for Genome Wide Association Studies

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

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.