analyzeSingleGenes: Analyze Single Genes

Description Usage Arguments Value Examples

View source: R/analyzeSingleGenes.R

Description

Obtains correlations and corGSEA results for each gene of interest

Usage

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analyzeSingleGenes(genesOfInterest, Species = c("hsapiens", "mmusculus"),
  GSEA_Type = c("simple"), Sample_Type = "normal", Tissue = "all",
  crossCompareMode = FALSE, nperm = 2000, TERM2GENE = NULL,
  whichCompareGroups = c("all", "normal", "cancer"),
  outputPrefix = "CorrelationAnalyzeR_Output", sampler = FALSE,
  runGSEA = TRUE, topPlots = TRUE, returnDataOnly = TRUE,
  pool = NULL, makePool = FALSE)

Arguments

genesOfInterest

A vector of genes to analyze.

Species

Species to obtain gene names for. Either 'hsapiens' or 'mmusculus'

GSEA_Type

Which GSEA annotations should be considered? Options listed in correlationAnalyzeR::pathwayCategories – See details of getTERM2GENE for more info.

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 genesOfInterest.

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 genesOfInterest. Run getTissueTypes() to see available tissues.

crossCompareMode

Instead of normal single gene analysis, will generate correlations for single gene across all tissue-disease groups. GSEA will not be run. Will only consider user input for returnDataOnly, whichCompareGroups, outputPrefix, Species, and genesOfInterest.

nperm

Number of permutations to run in GSEA. Default is 2000

TERM2GENE

Mapping of geneset IDs to gene names. If NULL, it will be generated automatically. Only applicable if GSEA is to be run.

whichCompareGroups

For crossCompareMode, select "all", "normal", or "cancer" to analyze correlations from the corresponding groups.

outputPrefix

Prefix for saved files. Should include directory info.

sampler

If TRUE, will only return 100,000 random genesets from either simple or complex TERM2GENEs. Useful for reducing GSEA computational burden.

runGSEA

If TRUE will run GSEA using gene correlation values.

topPlots

Logical. If TRUE, myGSEA() will build gsea plots for top correlated genesets.

returnDataOnly

if TRUE will return only a dataframe of correlation values and will not generate any folders or files.

pool

an object created by pool::dbPool to accessing SQL database. It will be created if not supplied.

makePool

Logical. Should a pool be created if one is not supplied? Default: FALSE.

Value

A named list of correlation values, corGSEA results, and visualizations for each gene of interest.

Examples

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genesOfInterest <- c("ATM", "SLC7A11")
correlationAnalyzeR::analyzeSingleGenes(genesOfInterest = genesOfInterest,
                              Species = "hsapiens", returnDataOnly = TRUE,
                              GSEA_Type = "simple",
                              Sample_Type = c("normal", "cancer"),
                              Tissue = c("respiratory", "pancreas"))

genesOfInterest <- c("Brca1")
correlationAnalyzeR::analyzeSingleGenes(genesOfInterest = genesOfInterest,
                              Species = "mmusculus",
                              GSEA_Type = "simple", returnDataOnly = TRUE,
                              crossCompareMode = TRUE,
                              whichCompareGroups = "normal")

millerh1/correlationAnalyzeR documentation built on Dec. 10, 2019, 1:31 a.m.