findCorrelation: Function to perfrom correlation analysis in TADs

In kokonech/InTAD: Search for correlation between epigenetic signals and gene expression in TADs

Description

This function combines genes and signals in inside of TADs

Usage

findCorrelation(object, method = "pearson", adj.pval = FALSE,
  plot.proportions = FALSE)

Arguments

object	InTADSig object with signals and genes combined in TADS
method	Correlation method: "pearson" (default), "kendall", "spearman"
adj.pval	Perform p-value adjsutment and include q-values in result
plot.proportions	Plot proportions of signals and genes in correlation

Value

A table with correlation values for signal-gene pairs including correlation p-value, euclidian distance and rank.

Examples

## perform analysis on test data
inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)
inTadSig <- filterGeneExpr(inTadSig, geneType = "protein_coding")
inTadSig <- combineInTAD(inTadSig, tadGR)
corData <- findCorrelation(inTadSig, method="pearson")

kokonech/InTAD documentation built on Jan. 1, 2021, 9:23 p.m.