gwas: gwas

In pezzcvd/daphneg2:

Description

it performs a gwas analysis. It collects all the input files: phenotype, genotype and, in case, covariate. Then through the software GEMMA it calculates the kinship matrix, and it performs the assosiaction analysis. Subsequently it adujsts the P-values of the associations, calculating FDRs and since the genotype table is based on a pruned SNP list (meaning that the SNPs that are inherited together with a target SNPs are filtered out) it eventually retrieves the lists of SNPs in the same LD units with the significant SNPs in the result table.

Usage

gwas(
  gemma.name,
  gw.input,
  gw.cv,
  gw.snp_annot,
  gw.gen_annot,
  gw.cov = NULL,
  gw.loco = F,
  gw.miss = 0.05,
  gw.maf = 0.05,
  gw.kinship = "",
  gw.pw = normalizePath("~")
)

Arguments

gemma.name	character1. Gemma executable name. Version or system may vary.
gw.input	character1. Parameter name, used as a prefix in the files of interest.
gw.cv	integer1. Number of covariates. Can be 0, 1 or 2 (in this case is meant >1).
gw.snp_annot	character1. Snp annotation file path.
gw.gen_annot	character1. Genome annotation file path.
gw.cov	character1. Covariate name, can be one specific covariate or "all". (defalut NULL)
gw.loco	boolean(1). Leave one chromosome out approach. (default FALSE)-.
gw.miss	missingness
gw.maf	minor allele frequency
gw.kinship	precomputed kinship file name, default ""
gw.pw	character1. Output path. (default home folder).

Value

NULL. It automatically performs the whole GWAS analysis procedure.

pezzcvd/daphneg2 documentation built on Oct. 13, 2021, 10:34 p.m.