rvmeta.readDataByGene {seqminer} | R Documentation |
Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.
rvmeta.readDataByGene(scoreTestFiles, covFiles, geneFile, geneName, multiAllelic = FALSE)
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
covFiles |
character vector, covaraite files (rvtests outputs using –meta cov) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
multiAllelic |
boolean, whether to read multi-allelic sites as multiple variants or not |
a list of statistics including chromosome, position, allele frequency, score statistics, covariance and annotation(if input files are annotated).
http://zhanxw.com/seqminer/ for online manual and examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer") covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer") geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer") cfh <- rvmeta.readDataByGene(scoreFileName, covFileName, geneFile, "CFH")