rvmeta.readDataByRange {seqminer} | R Documentation |
Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted.
rvmeta.readDataByRange(scoreTestFiles, covFiles, ranges, multiAllelic = FALSE)
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
covFiles |
character vector, covaraite files (rvtests outputs using –meta cov) |
ranges |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
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.readDataByRange(scoreFileName, covFileName, "1:196621007-196716634")