Description Usage Arguments Value Examples
Regress one phenotype on the given genes at a single marker.
1 2 |
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 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
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