getPair: getPair to extract pairInfo slot from Pair object.

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

getPair is a function to easily extract pairInfo out of a Pair object. By specifying geneID or probe, geneInfo for the defined genes (geneID ) and probes (probe) will be extracted out of Pair object.

Usage

getPair(object, probe, geneID)

## S4 method for signature 'Pair'
getPair(object, probe, geneID)

Arguments

object	Pair object
probe	A vector of probes' name. When specified, only the pair containing these probes will be output.
geneID	A vector of genes' id. When specified, only the pair containing these genes will be output.

Value

Pair information such as empirical P values, probe and gene ID.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

df <- data.frame(Probe=c("cg19403323","cg12213388","cg26607897"),
GeneID =c("ID255928","ID84451","ID55811"),
Symbol =c("SYT14","KIAA1804","ADCY10"),
Pe=c(0.003322259,0.003322259,0.003322259))
pair <- fetch.pair(pair = df)
Pairs <- getPair(pair, probe = "cg19403323") # get pair information for a probe
Pairs <- getPair(pair, geneID = "ID55811") # get pair information for a gene

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.