predict_signature {supersigs} | R Documentation

## Function to predict using SuperSig object

### Description

Using a generated SuperSig, predict on a new dataset and return predicted probabilities for each observation.

### Usage

    predict_signature(object, newdata, factor)

### Arguments

`object` | an object of class `SuperSig`
`newdata` | a data frame of mutations containing columns for `sample_id`, `age`, `IndVar`, and the 96 trinucleotide mutations (see vignette for details)
`factor` | the factor/exposure (e.g. "age", "smoking")

### Value

`predict_signature` returns the original data frame with additional columns for the feature counts and classification score

### Examples

    head(example_dt) # use example data from package
    input_dt <- make_matrix(example_dt) # convert to correct format
    input_dt$IndVar <- c(1, 1, 1, 0, 0) # add IndVar column
    out <- get_signature(data = input_dt, factor = "Age") # get SuperSig
    newdata <- predict_signature(out, newdata = input_dt, factor = "age")
    suppressPackageStartupMessages({library(dplyr)})
    head(newdata %>% select(score))

[Package supersigs version 1.0.0 Index]