extractData: extractData

In lea-urpa/MultiGWASTools: Tools for exploring and visualizing results from multiple GWAS analyses

Description

Connects to previously created database (currently only a MonetDBLite database created with makeDatabase) and queries specific data from the database. Essentially a wrapper for MonetDBLite query statements, without having to learn SQL query syntax. Users can provide either a vector of rsids to query the database with OR a vector of start/stop positions along a given chromosome. One can also threshold the data with minimum p value, test (additive or other), or phenotype.

Usage

extractData(dbdir, rsids = NULL, pos = NULL, pvalThresh = 1,
  phenotype = "all", test = "all", dbtype = "MonetDB")

Arguments

dbdir	A string giving the directory (filepath + folder name) of the database to connect to. The file path must be absolute, not relative (eg no "./").
rsids	A vector containing the rsids to query the database. Must provide either rsids or positions, not both!
pos	A vector containing three numbers, the chromosome, start and stop positions along that chromosome to query the database. Must provide either rsids or positions, not both!
pvalThresh	A number indicating the minimum threshold of pvalues for the data to return, by default all (pvalue = 1).
phenotype	A string or vector of strings containing the phenotypes that will be extracted from the data, by default all phenotypes.
test	A string or vector of strings containing the tests that will be extracted from the data, by default all tests.
dbtype	A string indicating database type. Currently only the default "MonetDB" accepted.

lea-urpa/MultiGWASTools documentation built on May 24, 2019, 5:01 a.m.