log2transform: Transform values

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Transform values

Description

Transform values

Usage

log2transform(
  object,
  assay = assayNames(object)[1],
  pseudo = 0,
  verbose = FALSE
)

exp2(object, verbose = FALSE)

zscore(object, verbose = FALSE)

sscale(mat, verbose = FALSE)

fscale(mat, verbose = FALSE)

quantnorm(object, verbose = FALSE)

invnorm(object, verbose = FALSE)

vsn(object, verbose = FALSE, delog = TRUE)

Arguments

object	SummarizedExperiment
assay	character vector : assays for which to perform transformation
pseudo	number : pseudo value to be added prior to transformation
verbose	TRUE or FALSE : whether to msg
mat	matrix
delog	TRUE or FALSE (vsn)

Value

Transformed sumexp

Examples

file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
object <- read_maxquant_proteingroups(file)

object                       %>% plot_sample_densities()
invnorm(object)              %>% plot_sample_densities()

object                       %>% plot_sample_densities()
quantnorm(object)            %>% plot_sample_densities()

object                       %>% plot_sample_densities()
#vsn(object)                  %>% plot_sample_densities()  # dataset too small

object                       %>% plot_sample_densities()
zscore(object)               %>% plot_sample_densities()

object                       %>% plot_sample_densities()
exp2(object)                 %>% plot_sample_densities()
log2transform(exp2(object))  %>% plot_sample_densities()

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.