xMER Documentation

Function to perform eQTL analysis using MatrixEQTL

Description

xME is supposed to perform eQTL analysis using MatrixEQTL.

Usage

xME(expression, genotype, GR.Gene, GR.SNP, mode = c("cis", "both",
"none"), distance.cis = 1e+06, pvalue.cis = 0.01,
pvalue.trans = 1e-05, num.PCs = 0, mydir = tempdir(check = T),
verbose = T, silent = F)

Arguments

expression

a data matrix/frame with genes in rows and samples in columns

genotype

a data (sparse) matrix/frame with SNPs in rows and samples in columns

GR.Gene

an GR object storing the genomic regions of genes

GR.SNP

an GR object storing the genomic regions of SNPs

mode

a character specifying the eQTL mode. It can be 'cis' for cis-eQTL analysis, 'both' for both cis-eQTL and trans-eQTL analysis, and 'none' (no eQTL analysis only returning variables actually used for eQTL analysis: expression, genotype, GR.Gene and GR.SNP)

distance.cis

a distance defining cis-eQTL. By default, it is 1Mb

pvalue.cis

the p-value threshold outputing the cis-eQTL. By default, it is 1e-2

pvalue.trans

the p-value threshold outputing the trans-eQTL. By default, it is 1e-5

num.PCs

an integer specifying the number of principle components (PCs) used for expression being regressed out. If zero (by default), no gression is done

mydir

a temporary directory file

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display

silent

logical to indicate whether the messages will be silent completely. By default, it sets to false. If true, verbose will be forced to be false

Value

a "MatrixEQTL" object, a list including componets 'cis' and 'trans' (if mode is 'both'). The 'cis' (or 'trans') contains a data frame 'eqtls' with following columns ("snps","gene","statistic","pvalue","FDR","beta"). If the mode is 'none', return a list with four components 'expression', 'genotype', 'GR.Gene' and 'GR.SNP'

Note

none

See Also

xRegress

Examples

## Not run: 
# Load the library
library(XGR)
res <- xME(expression, genotype, GR.Gene, GR.SNP, mode='none')

## End(Not run)