denovolyzeMultiHits {denovolyzeR} | R Documentation |
Determine significance of genes with multiple de novos
Description
Are there more genes containing >1 de novos than expected?
Usage
denovolyzeMultiHits(genes, classes, nsamples, nperms = 100,
includeGenes = "all", includeClasses = c("syn", "mis", "lof", "prot",
"all"), nVars = "actual", geneId = "geneName", probTable = NULL,
misD = NULL, signifP = 3, roundExpected = 1)
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. |
nperms |
Number of permutations |
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. |
nVars |
Select whether expected number of multihits is determined by "expected" total number of variants , or "actual" total. Actual (default) is more conservative. |
geneId |
Gene identifier used. One of "hgncID", "hgncSymbol", "enstID", "ensgID" or "geneName" (default, equals ensembl "external_gene_name") |
probTable |
Probability table. A user-defined table of probabilities can be provided here, to replace the probability table included in the package. |
misD |
If the user-specified probability table contains probabilities for a sub-category of missense variants (e.g. predicted to be damaging by an in silico algorithm), this column should be called misD, or the alternative name should be specified here. |
signifP |
Number of significant figures used to round p-values in output. |
roundExpected |
Number of decimal places used to round expected burdens in output. |
Details
See vignette (denovostats_intro) for more information.
Value
Returns a data.frame
Examples
denovolyzeMultiHits(genes=autismDeNovos$gene,
classes=autismDeNovos$class,
nsamples=1078)