fetch.pair: fetch.pair to generate Pair class object.

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

Description

fetch.pair is a funtion to take in enhancer-gene linkage prediction information, probe information and gene annotation generating a Pair class object, which is the input for plotting functions. Options (pair, probeInfo, geneInfo) can take in R object or read files by specifying file paths.

Usage

fetch.pair(pair, probeInfo, geneInfo)

Arguments

pair	A data.frame (R object) or a path of XX.csv file containing pair information such as output of function get.pair.
probeInfo	A GRnage object or a path of XX.rda file which only contains a GRange of probe information.
geneInfo	A GRnage object or path of XX.rda file which only contains a GRange of gene information such as Coordinates, GENEID and SYMBOL.

Value

A Pair class object containing 3 slots. Detail see Pair-class

Author(s)

Lijing Yao (maintainer: [e-mail])

See Also

schematic.plot

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))
geneInfo <- txs()
## input can be a path
pair <- fetch.pair(pair = df, geneInfo=geneInfo)

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