rvmeta.readDataByRange: Read association statistics by range 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 range from METAL-format files. Both score statistics and covariance statistics will be extracted.

Description

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

Usage

rvmeta.readDataByRange(scoreTestFiles, covFiles, ranges, 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)
ranges	character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index
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.readDataByRange(scoreFileName, covFileName, "1:196621007-196716634")

seqminer documentation built on Oct. 7, 2024, 1:15 a.m.