compareReg2Traits: Compare two objects of genomic region~gene~trait associations

In BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

Description

This function reports per trait number of reported genomic region~gene~trait from two different objects.

Usage

compareReg2Traits(interactionsTraits, interactionsTraits2,
  traitID = c("Trait", "Trait"), naming = c("Trait1", "Trait2"))

Arguments

interactionsTraits	A GInteractions object, likely produced by [reg2trait]. This object stores info about genomic region~gene~trait associations, as follows: anchor1 corresponds to genomic region (likely SNP location), anchor2 corresponds to gene location, and gene symbol and associated disease is stored as a meta-data.
interactionsTraits2	A GInteractions object, likely produced by [reg2trait]. This object stores info about genomic region~gene~trait associations, as follows: anchor1 corresponds to genomic region (likely SNP location), anchor2 corresponds to gene
traitID	character vector of length 2 which stores information about column names where trait info are stored for both input objects. By default c("Trait","Trait")
naming	a character vector (default: c("Traits1,"Trait2"). Column names in the output object.

Details

For each trait that is present in at least one of the interactionsTraits GInteractions objects report how many associated genes is present in the first GInteractions object, and how many is present in the 2nd GInteractions object. It allows an easy identification of traits for which [reg2gene] analysis improved number of disease associated genes.

Value

a matrix with rows corresponding to traits, and two columns with info about gene counts for these traits. Each column gathers info from one interactionsTraits GInteractions object (variant~gene interactions + trait association stored as meta-data).

Author(s)

Inga Patarcic

Examples

library(GenomicRanges)
library(InteractionSet)

# 1. creating interaction object 1 with added diseases 

GRReg1_toyDisease <- GRReg1_toy
GRReg1_toyDisease$disease <- paste0("dis",c(1,1,3:(length(GRReg1_toy))))

 
# 2. creating interaction object 2 with added diseases 
GRReg2_toyDisease <- GRReg2_toy
GRReg2_toyDisease$disease <- paste0("dis",1:length(GRReg2_toy))


# comparing them with compareReg2Traits
compareReg2Traits(interactionsTraits=GRReg1_toyDisease,
                  interactionsTraits2=GRReg2_toyDisease,
                  traitID=c("disease","disease"),
                  naming=c("Trait1","Trait2"))
 

BIMSBbioinfo/reg2gene documentation built on May 3, 2019, 6:42 p.m.