PermuteMultiHits {denovolyzeR}

Permutes x variants across a genelist, and counts genes with multiple hits

Description

An internal function called by denovolyzeMultiHits

Usage

PermuteMultiHits(x, y, nperms = 100, class = "lof", geneId = "geneName",
  includeGenes = "all", probTable = pDNM)

Arguments

x

Total number of de novo variants observed in dataset

y

Number of genes with >1 de novo variant (of class "class") in the population

nperms

Number permutations

class

In c("lof","mis","syn","prot")

geneId

Gene identifier used. One of "hgncID", "hgncSymbol", "enstID", "ensgID" or "geneName" (default, equals ensembl "external_gene_name")

includeGenes

Genes to include in analysis. "all" or a vector of gene names.

probTable

Probability table. A user-defined table of probabilities can be provided here, to replace the probability table included in the package.

Value

Returns a named vector of 5 values

See Also

denovolyzeMultiHits