get_processedExprSet: Building ExpressionSet Object with preprocess

In HuaZou/MyRtools: Statistic Approaches on Data Analysis

Description

precessing the ExpressionSet object by filtering, transforming or normalization

Usage

get_processedExprSet(dataset=ExpressionSet,
        trim_cutoff=0.2,
        trim=c("none", "both", "feature", "sample", "Group"),
        transform=c("none", "log2", "log2p", "log10", "log10p"),
        normalize=c("none", "TSS", "TMM", "RLE", "CLR", "Zscore", "Median", "MAD", "Robust", "Unit", "Min_Max"),
        impute=c("none", "deletion", "GlobalStandard", "KNN"))

Arguments

dataset,	ExpressionSet; (Required) an Raw ExpressionSet object by 'get_ExprSet'.
trim_cutoff,	Numeric; the threshold for filtering (default: Cutoff=0.2).
trim,	Character; filter to apply.(default: trim="none").
normalize,	Character; normalization to apply.(default: normalize="none").
tranform,	Character; transformation to apply.(default: tranform="none").
inpute,	Character; inputation to apply.(default: inpute="none").

Details

12/7/2021 Guangzhou China

Value

an preprocessed ExpressionSet Object

Author(s)

Hua Zou

Examples

library(dplyr)
data("ExprSetRawRB")
ExprSet <- get_processedExprSet(dataset=ExprSetRawCount,
trim_cutoff=0.2,
trim="Group",
transform="log2",
normalize=NULL,
impute=NULL)

HuaZou/MyRtools documentation built on Jan. 6, 2022, 8:56 a.m.