xMEbesd | R Documentation |
xMEbesd
is supposed to store eQTL summary data in the BESD
format ready for the use in SMR.
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)
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 |
a logical vector
This function requires the software 'smr' at http://cnsgenomics.com/software/smr. Shell command lines in Terminal (Mac and Linux) are:
1a) Mac: wget
http://cnsgenomics.com/software/smr/download/smr_Mac.zip && unzip
smr_Mac.zip && mv smr_Mac ~/smr
1b) Linux: wget
https://cnsgenomics.com/software/smr/download/smr_Linux.zip && unzip
smr_Linux.zip && mv smr_Linux ~/smr
2a) # Assuming a ROOT (sudo) privilege: sudo cp ~/smr
/usr/local/bin
2b) # Assuming without ROOT (sudo) privilege and adding the
system PATH variable to your ~/.bash_profile file: export
PATH=$HOME:$PATH
xMEbesd
## 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)