getCorrelationData: Get Gene Correlation Data

In Bishop-Laboratory/correlationAnalyzeR: Generate Novel Insights from Gene Correlation Data

Get Gene Correlation Data

Description

Obtain correlation data by querying MySQL database

Usage

getCorrelationData(Sample_Type, Tissue, geneList, corrMat = NULL, pool = NULL)

Arguments

Sample_Type	Type of RNA Seq samples used to create correlation data. Either "all", "normal", or "cancer". Can be a single value for all genes, or a vector corresponding to geneList. Not used if corrMat is set.
Tissue	Which tissue type should gene correlations be derived from? Default = "all". Can be a single value for all genes, or a vector corresponding to geneList. Not used if corrMat is set. Run getTissueTypes() to see available tissue list.
geneList	Vector of genes for which data will be extracted.
corrMat	A custom correlation matrix generated by generateCorrelations() to use instead of pre-supplied databases.
pool	an object created by pool::dbPool to accessing SQL database. It will be created if not supplied. Not used if corrMat is set.

Value

A correlation data frame object

Examples

corrData <- correlationAnalyzeR::getCorrelationData(Sample_Type = "normal",
                                       Tissue = "kidney",
                                       geneList = c("ATM", "BRCA1"))

Bishop-Laboratory/correlationAnalyzeR documentation built on June 28, 2022, 8:31 p.m.