predDNM: A function to predict de novo SNVs from features produced by...

In mbelmadani/forestDNM-archive: Predicts de novo SNVs when provided a VCF containing variants of a genotyped family.

Usage

predDNM(X, rf, cutoff = 0.2)

Arguments

X
rf
cutoff

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (X, rf, cutoff = 0.2) 
{
    info = X[, colnames(X) %in% c("chr", "pos", "par_allele", 
        "mut_allele")]
    X = X[, !colnames(X) %in% c("chr", "pos", "par_allele", "mut_allele")]
    info$prd = predict(rf, X, type = "prob")[, 1]
    info = info[info$prd >= cutoff, ]
    return(info)
  }

mbelmadani/forestDNM-archive documentation built on May 30, 2019, 2:17 p.m.