mediate: Regress one phenotype on the given genes at a single marker.
In dmgatti/qtl2med: Mediation Analysis for qtl2

Description Usage Arguments Value Examples

Regress one phenotype on the given genes at a single marker.

1 2	mediate(pheno, chr, pos, type = c("haplo", "snp"), expr, ensembl, genoprobs, addcovar, cc_dbfile)

`pheno:`	numeric matrix with one column. Sample IDs must be in rownames and must match rownames in genoprobs.
`chr:`	character containing a single chromosome ID.
`pos:`	numeric value indicating the position in Mb at which to mediate.
`type:`	character value that is either 'haplo' or 'snp', indicating which type of genotype values to mediate upon.
`expr:`	numeric matrix containing the gene expression values. Sample names in rownames and Ensembl IDs in colnames.
`ensembl:`	data.frame containing gene annotation as obtained from `get_ensembl_gene`.
`genoprobs:`	list containing 3-dimensional arrays of allele probs, one for each chromosome. In qtl2 format. Samples in rows, 8 founders in columns, markers in slices.
`addcovar:`	numeric matrix of additive covariates without the intercept. Sample IDs must be in rownames. Typically creates using model.matrix(~covar1 + covar2, data = data).
`cc_dbfile:`	full path to the CC_SNP database file created by Karl Broman.

data.frame containing the mediation results.

data(pheno)
data(genoprobs)
data(map)
data(addcovar)
data(expr)
chr = 13
pos = 112.205823
build = 90
ensembl = get_ensembl_genes(chr = chr, build = build)
          med = mediate(pheno = pheno,
          chr = chr,
          pos = pos,
          type = "haplo",
          expr = dataset.islet.rnaseq$expr,
          ensembl = ensembl,
          genoprobs = genoprobs,
          addcovar = addcovar)