rvmeta.readDataByGene: Read association statistics by gene from METAL-format files....

In seqminer: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.

Description

Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.

Usage

rvmeta.readDataByGene(
  scoreTestFiles,
  covFiles,
  geneFile,
  geneName,
  multiAllelic = FALSE
)

Arguments

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

Value

a list of statistics including chromosome, position, allele frequency, score statistics, covariance and annotation(if input files are annotated).

See Also

http://zhanxw.com/seqminer/ for online manual and examples

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")

seqminer documentation built on Sept. 2, 2023, 9:08 a.m.