parseInput {denovolyzeR}

Checks input for errors

Description

An internal function to check inputs

Usage

parseInput(genes = genes, classes = classes, nsamples = nsamples,
  groupBy = groupBy, includeGenes = includeGenes,
  includeClasses = includeClasses, geneId = geneId, signifP = signifP,
  roundExpected = roundExpected, probTable = NULL)

Arguments

genes

A vector of genes containing de novo variants.

classes

A vector of classes of de novo variants. Standard supported classes are "syn" (synonymous), "mis" (missense), "non" (nonsense), "splice" (splice), "frameshift" (frameshift) and "lof" (loss of function = non + splice + frameshift). Additional classes that are supported by the code, but are not included in the built-in probability tables, are "stoploss","startloss", "misD" (damaging missense). These labels may be used for user-supplied probability tables. If "misD" is present, then "mis" (in the input) implies non-damaging missense.

nsamples

Number of individuals considered in de novo analysis.

groupBy

Results can be tabulated by "gene", or by variant "class"

includeGenes

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

includeClasses

Determines which variant classes are tabulated in output. In addition to the input classes, summaries can be produced for "prot" (protein-altering = mis + lof), "all", and "protD" (protein damaging = misD + lof, only available if misD included in user-specified probability table). If "misD" is present, then "mis" will return statistics for all missense. Non-damaging missense are not analysed separately.

geneId

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

signifP

Number of significant figures used to round p-values in output.

roundExpected

Number of decimal places used to round expected burdens in output.

probTable

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

Value

warning or error if any invalid input, else assigns variables back to parent function