TransformExpValues {MARVEL} | R Documentation |
Transform gene expression Values
Description
Transforms gene expression values and censor lowly-expressing genes.
Usage
TransformExpValues(
MarvelObject,
offset = 1,
transformation = "log2",
threshold.lower = 1
)
Arguments
MarvelObject |
Marvel object. S3 object generated from |
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 |
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 |
Value
An object of class S3 with updated slot MarvelObject$Exp
.
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
)
[Package MARVEL version 1.4.0 Index]