ScanAnnotationSQLite-class: Class ScanAnotationSQLite

In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description

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

Constructor

ScanAnnotationSQLite(dbpath):

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

• "scanID": vector containing unique scan ids.

If a column representing sex is present, it must have the following format:

• "sex": character vector with values 'M' or 'F'.

"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 ScanAnnotationSQLite constructor creates and returns a ScanAnnotationSQLite instance.

Accessors

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

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

close(object): Closes the database connection.

nscan(object): The number of scans in the database.

getScanID(object, index, condition): A unique vector of scan 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 sex='M'").

getSex(object, index, condition): A character vector of sex, with values 'M' or 'F'. 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.

hasSex(object): Returns TRUE if the column 'sex' is present in object.

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 sex='M'"). 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 scan annotation table. value must be a data.frame containing a column "scanID".

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

Author(s)

Stephanie Gogarten

See Also

SnpAnnotationSQLite, ScanAnnotationDataFrame, GenotypeData, IntensityData

Examples

library(GWASdata)
dbpath <- tempfile()
scanAnnot <- ScanAnnotationSQLite(dbpath)

data(illumina_scan_annot)
writeAnnotation(scanAnnot, illumina_scan_annot)

# list columns
vars <- getVariableNames(scanAnnot)

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

scanID <- getScanID(scanAnnot)
sex <- getSex(scanAnnot)
if (hasVariable(scanAnnot, "plate")) plate <- getVariable(scanAnnot, "plate")
subjectID <- getVariable(scanAnnot, "subjectID", condition="WHERE sex='M'")

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

close(scanAnnot)
file.remove(dbpath)

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