log2transform | R Documentation |
Transform values
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)
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) |
Transformed sumexp
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()
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