import_SE: Convert inputs into SummarizedExperiment object

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Convert inputs into SummarizedExperiment object

Description

Convert inputs into SummarizedExperiment object.

Usage

import_SE(
    object,
    rowdata = NULL,
    rowranges = GRangesList(),
    coldata = NULL,
    metadata = list())

Arguments

object	(Required). matrix-like, features table with expressed values (row: featureID; columns: samples).
rowdata	(Optional). DataFrame, A DataFrame object describing the rows (default: NULL).
rowranges	(Optional). A GRanges or GRangesList object describing the ranges of interest. (default: NULL).
coldata	(Optional). DataFrame, An optional DataFrame describing the samples (default: NULL).
metadata	(Optional). List, An optional list of arbitrary content describing the overall experiment (default: NULL).

Details

The profile of inputs is a feature table of RNA-seq or metabolites or others: A matrix with rows corresponding to features and columns to samples, in which the value of each entry is the number of times that features was observed in that sample.

Value

SummarizedExperiment::SummarizedExperiment object hold expressed profile, information related row and column or experimental design.

Author(s)

Created by Hua Zou (1/8/2023 Shenzhen China)

Examples

## Not run: 
data("Zeybel_2022_protein")
assay <- SummarizedExperiment::assay(Zeybel_2022_protein) %>%
  data.frame()
rowData <- SummarizedExperiment::rowData(Zeybel_2022_protein) %>%
  data.frame()
colData <- SummarizedExperiment::colData(Zeybel_2022_protein) %>%
  data.frame()
metadata <- list(lab="hua", type="protein")

assay <- assay[1:10, 1:10]
import_SE(
    object = assay,
    rowdata = rowData,
    coldata = colData,
    metadata = metadata)

## End(Not run)

HuaZou/MicrobiomeAnalysis documentation built on Dec. 12, 2023, 10:37 a.m.