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.