matrix2sumexp {autonomics}R Documentation

Convert matrix into SummarizedExperiment

Description

Convert matrix into SummarizedExperiment

Usage

matrix2sumexp(
  x,
  sdt = NULL,
  sdtby = if (is.null(sdt)) NULL else names(sdt)[1],
  subgroupvar = NULL,
  fdt = NULL,
  fdtby = if (is.null(fdt)) NULL else names(fdt)[1],
  fnamevar = NULL,
  verbose = TRUE
)

Arguments

x

matrix

sdt

sample data.table / data.frame / DataFrame

sdtby

sample data mergeby column

subgroupvar

string / NULL

fdt

feature data.table / data.frame / DataFrame

fdtby

feature data mergeby column

fnamevar

string / NULL

verbose

TRUE/FALSE

Value

SummarizedExperiment

Examples

require(magrittr) 
file <- download_data('atkin18.metabolon.xlsx')
x <- values(read_metabolon(file, plot=FALSE))
object <- matrix2sumexp(x)
object %<>% pca()
biplot(object, nloadings=0, color=subgroup)

[Package autonomics version 1.2.0 Index]