xME | R Documentation |
xME
is supposed to perform eQTL analysis using MatrixEQTL.
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)
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 |
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'
none
xRegress
## Not run: # Load the library library(XGR) res <- xME(expression, genotype, GR.Gene, GR.SNP, mode='none') ## End(Not run)