evaluate: Calculates prognostic statistics based on m2eQTLs.
In jeffreyat/M2EFM: M2EFM

Calculates prognostic statistics based on m2eQTLs.

evaluate(meth = NULL, exp = NULL, clin = NULL, eqtls = NULL,
  gene_type = NULL, covariates = c(), gene_sig = NULL, gene_seed = NULL,
  genes = NULL, num_genes = NULL, num_probes = NULL,
  intersect_data = FALSE, integrate_data = FALSE, single_data = "exp",
  time_to_event_col = NULL, event_col = NULL, rescale = TRUE,
  monte_carlo_size = 100, training_prop = 0.7, pam50risk = NULL,
  val = list(), val_clin = list(), val_pam50 = list(), alpha = 0)

`meth`	a MethylationData object, or a data.frame with DNA methylation Beta-values
`exp`	an ExpressionData object, or a data.frame with gene expression values
`clin`	a data.frame of clinical data for both meth and exp samples
`eqtls`	object returned from get_m2eqtls()
`gene_type`	type of gene list being provided ("trans", "cis", "random", "pre") where trans and cis are those types of m2eQTLs and random is a random set of genes
`covariates`	a vector of covariates to include from the clinical data
`gene_sig`	file to store the gene list in (or load it from)
`gene_seed`	random seed to generate random gene list from
`num_genes`	number of genes to use for a random gene list
`num_probes`	number of probes to use for a random probe list
`intersect_data`	whether to intersect samples for meth and exp (automatically done if integrate_data=TRUE)
`integrate_data`	whether or not to integrate meth and exp values into a single data frame for the model
`single_data`	which single data type to use if integrate_data=FALSE, can be "exp" or "meth"
`time_to_event_col`	name of column with time to event
`event_col`	name of column with sample event status, or outcome for binomial models
`monte_carlo_size`	how many random splits of the training data to perform
`training_prop`	proportion of the data to use for training
`val`	a list of validation data sets (list of data.frame objects, with combined methylation and expression values or just one or the other)
`val_clin`	a list of validation clinical data, parallel to val
`alpha`	a value in [0,1] where 0 is Ridge penalty and 1 is LASSO