glmm.score.meta {GMMAT} | R Documentation |
Performing meta-analysis for GLMM based score test results
Description
Use output files from GLMM based score tests to perform meta-analysis.
Usage
glmm.score.meta(files, outfile, SNP = rep("SNP", length(files)),
A1 = rep("A1", length(files)), A2 = rep("A2", length(files)))
Arguments
files |
a vector of input file names. The input files should be the output files of |
outfile |
the output file name. |
SNP |
a character vector of SNP column names in each input file. The length and order must match the length and order of |
A1 |
a character vector of allele 1 column names in each input file. The length and order must match the length and order of |
A2 |
a character vector of allele 2 column names in each input file. The length and order must match the length and order of |
Value
a data frame containing the following:
SNP |
SNP name. |
A1 |
allele 1. |
A2 |
allele 2. |
N |
total sample size. |
AF |
effect allele frequency (user-defined: can be either allele 1 or allele 2). |
SCORE |
the summary score of the effect allele. |
VAR |
the variance of the summary score. |
PVAL |
meta-analysis p-value. |
Author(s)
Han Chen
See Also
Examples
infile1 <- system.file("extdata", "meta1.txt", package = "GMMAT")
infile2 <- system.file("extdata", "meta2.txt", package = "GMMAT")
infile3 <- system.file("extdata", "meta3.txt", package = "GMMAT")
outfile <- tempfile()
glmm.score.meta(files = c(infile1, infile2, infile3), outfile = outfile,
SNP = rep("SNP", 3), A1 = rep("A1", 3), A2 = rep("A2", 3))
unlink(outfile)