xMEbesdR Documentation

Function to store eQTL summary data in the BESD format

Description

xMEbesd is supposed to store eQTL summary data in the BESD format ready for the use in SMR.

Usage

xMEbesd(summary, contexts = c("CD14", "LPS2", "LPS24", "IFN", "Bcell",
"NK", "Neutrophil", "Monocyte", "Blood", "CD4", "CD8", "shared_CD14",
"shared_IFN", "shared_LPS2", "shared_LPS24"), outdir = ".",
clear = T, verbose = T)

Arguments

summary

a data frame storing eQTL summary statistics. It must contain columns 'context', and columns ('snp_cse','snps','effect_allele','other_allele','effect_maf') for the esi file, and columns ('gene_cse','gene','Symbol') for the epi file, and columns ('snps','gene','beta','statistic','pvalue','FDR') for the besd file

contexts

a vector specifying contexts included

outdir

the output directory. By default it is '.'

clear

logical to indicate whether the temporary and log files are cleared up. By default, it sets to TRUE

verbose

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

Value

a logical vector

Note

This function requires the software 'smr' at http://cnsgenomics.com/software/smr. Shell command lines in Terminal (Mac and Linux) are:

See Also

xMEbesd

Examples

## Not run: 
# Load the library
library(XGR)
summary <- xRDataLoader('JK_cohort_xMEdb',
RData.location=RData.location)
xMEbesd(summary, contexts="CD14", outdir="Pi_eQTL_hg19")

## End(Not run)