MARVEL (version 1.4.0)

TransformExpValues: Transform gene expression Values

Description

Transforms gene expression values and censor lowly-expressing genes.

Usage

TransformExpValues(
  MarvelObject,
  offset = 1,
  transformation = "log2",
  threshold.lower = 1
)

Value

An object of class S3 with updated slot MarvelObject$Exp.

Arguments

MarvelObject

Marvel object. S3 object generated from CheckAlignment function.

offset

Numeric value. To indicate the value to add to the expression values before log transformation. The only option for this argument is 1.

transformation

Character string. To indicate the type of transformation to use on the expression values after offsetting the values. The only option for this argument is log2.

threshold.lower

Numeric value. To indicate the value below which the expression values will be censored, i.e. re-coded as 0, after offsetting and transforming the values. The only option for this argument is 1.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- TransformExpValues(MarvelObject=marvel.demo,
                                  offset=1,
                                  transformation="log2",
                                  threshold.lower=1
                                  )