parseInput: Checks input for errors

In denovolyzeR: Statistical Analyses of De Novo Genetic Variants

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

denovolyzeR documentation built on May 2, 2019, 12:43 p.m.