geneVsGeneListAnalyze: Analyze gene vs gene list relationship

Description Usage Arguments Value Examples

View source: R/analyzeGeneVsGeneList.R

Description

Explores how a list of secondary genes relates to a primary gene of interest

Usage

1
2
3
4
5
6
7
geneVsGeneListAnalyze(pairedGenesList, Species = c("hsapiens",
  "mmusculus"), Sample_Type = c("normal", "cancer"), Tissue = "all",
  outputPrefix = "CorrelationAnalyzeR_Output", plotLabels = TRUE,
  sigTest = TRUE, nPerm = 2000, plotMaxMinCorr = TRUE,
  onlyTop = FALSE, topCutoff = 0.5, autoRug = TRUE,
  plotTitle = TRUE, returnDataOnly = TRUE, pool = NULL,
  makePool = FALSE)

Arguments

pairedGenesList

A list, named with primary genes of interest with vectors of secondary genes to test against OR a string containing the official MSIGDB name for a gene set of interest.

Species

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

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.

outputPrefix

Prefix for saved files. Should include directory info.

plotLabels

If TRUE, correlation histograms will contain labeled lines showing secondary genes and their correlation values. If list of secondary genes is large, set this to FALSE or onlyTop to TRUE to avoid cluttering the plot. Default: TRUE.

sigTest

Should the results be compared against random? Default: TRUE.

nPerm

Number of bootstrap sampling events to run during sigTest. Default: 2000.

plotMaxMinCorr

If TRUE, the top correlated and anti-correlated genes will be plotted alongside the selected secondary genes. Default: TRUE.

onlyTop

For larger secondary gene lists – This will filter the number of secondary genes which are plotted to avoid clutter if plotLabels = TRUE. Default: FALSE.

topCutoff

The value used for filtering if 'onlyTop' is 'TRUE'. Default: .5

autoRug

If the size of a secondary gene list > 50, plot lines will be replaced by an auto-generated rug. Default: TRUE.

plotTitle

Logical. If TRUE, plot title will be added to visualizations. Default: TRUE.

returnDataOnly

if TRUE will only return a list containing correlations and significance testing results if applicable. Default: TRUE.

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 list containing correlation values and signficance testing results

Examples

1
2
3
4
5
6
7
pairedGenesList <- list("TP53" = c("BRCA1", "CDK12", "PARP1"),
                        "SON" = c("AURKB", "SFPQ", "DHX9"))

correlationAnalyzeR::geneVsGeneListAnalyze(pairedGenesList = pairedGenesList,
                              Species = "hsapiens", returnDataOnly = TRUE,
                              Sample_Type = "normal",
                              Tissue = "brain")

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