findCorrelation: Function to perfrom correlation analysis

Description Usage Arguments Value Examples

View source: R/findCorrelation.R

Description

This function combines genes and signals in inside of TADs

Usage

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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

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## 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 Dec. 6, 2018, 2:08 p.m.