get_ExprSet: Building ExpressionSet Object
In HuaZou/MyRtools: Statistic Approaches on Data Analysis

Description Usage Arguments Details Value Author(s) Examples

View source: R/preprocess_ExpressionSet.R

ExpressionSet object comprising not only expressiondata but also metadata is very convenient to perform data analysis.

get_ExprSet(profile=Profile,
                  metadata=Metadata,
                  feature=Feature,
                  name="",
                  lab="",
                  contact="",
                  title="",
                  abstract="",
                  url="",
                  notes="")

`profile,`	Numeric matrix; (Required)a Matrix of expression data, whose Row is FeatureID and Column is SampleID.
`metadata,`	Data.frame; (Required)a dataframe. of Metadata(1st column must be "SampleID"), containing Group information and also environmental factors(biological factors).
`feature,`	Data.frame; the feature of Profile(default: Feature=NULL).
`name,`	Character; name of experimentData, inheriting from ExpressionSet(default: name="").
`lab,`	Character; lab of experimentData(default: lab="").
`contact,`	Character; contact of experimentData(default: contact="").
`title,`	Character; title of experimentData(default: title="").
`abstract,`	Character; abstract of experimentData(default: abstract="").
`url,`	Character; url of experimentData(default: url="").
`notes,`	Character; notes of experimentData(default: notes="").

12/2/2021 Guangzhou China

an ExpressionSet Object

Hua Zou

library(dplyr)
Profile <- data.table::fread(system.file("extdata", "Species_relative_abundance.tsv", package="MyRtools"))  %>% tibble::column_to_rownames("V1")
Metadata <- read.csv(system.file("extdata", "Metadata.csv", package="MyRtools"))
Feature <- read.csv(system.file("extdata", "Species_feature.csv", package="MyRtools")) %>% tibble::column_to_rownames("Species")

ExprSet <- get_ExprSet(profile=Profile,
                       metadata=Metadata,
                       feature=Feature,
                       name="Hua Zou",
                       lab="UCAS",
                       contact="zouhua1@outlook.com",
                       title="Experiment",
                       abstract="Profile",
                       url="www.zouhua.top",
                       notes="Expression")