PoolReplicate: Pool the replicated gene symbols

In metaOmic/preproc: Preprocessing of Normalized Gene Expression Data

Description

Pool the replicated gene symbols to one using the method "IQR", "largest", or "average".

Usage

PoolReplicate(dataset, method = REPLICATE.IQR)

Arguments

dataset	A numeric matrix of gene expressions without missing values or a Study object. For matrix, each row is for one gene and each column is for one sample. The row names are gene symbols. If dataset is Study object, the same rule applies to the matrix in Study@datasets.
method	A character string of the method to deal with the replicated gene symbols. It can be "IQR", "largest", or "average". The default is "IQR". See details.

Details

method can be "IQR", "largest", or "average".

IQR
			Represent the target gene symbol using the genes that presented the greatest inter-quartile range (IQR). This method has been recommended in Bioconductor.
largest
			Represent the target gene symbol using the largest expression.
average
			Represent the target gene symbol using the average of the expressions.

Value

A numeric matrix of gene expressions without replicated gene symbols. Each row is for one gene and each column is for one sample. The row names are gene symbols.

Author(s)

Lin Wang, Schwannden Kuo

Examples

data(datasets.eg)
data(preproc.option)
# PoolReplicate for matrix
mydata <- Annotate(datasets.eg[[1]], id.type=ID.TYPE.probeID,
                   platform=PLATFORM.hgu133plus2)
mydata <- Impute(mydata)
res  <- PoolReplicate(mydata, method=REPLICATE.IQR)
# PoolReplicate for Study
study <- new("Study", name="test", dtype=DTYPE.microarray, datasets=datasets.eg[1])
study <- Annotate(study, id.type=ID.TYPE.probeID, platform=PLATFORM.hgu133plus2)
study <- Impute(study)
res  <- PoolReplicate(mydata, method=REPLICATE.IQR)

metaOmic/preproc documentation built on May 22, 2019, 6:54 p.m.