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DESeqExpr

Provides a gene expression matrix using DESeq.

You can use HTSeqBam2Counts to prepare the suitable inputs for this function.

Version	1.0
Bundle	sequencing
Categories	Expression Short-read Sequencing
Authors	Marko Laakso (marko.laakso@significo.fi)
Issue tracker	View/Report issues
Requires	R ; DESeq2 (R-bioconductor)
Source files	component.xml DESeqExpr.r
Usage	Example with default values DESeqExpr( geneCounts = TextFile, //sampleNames = CSV, add1 = false, colIn = "", colOut = "", counts = false, maxNA = 1.00, normalized = true )

Inputs

Name	Type	Mandatory	Description
geneCounts	Array<TextFile>	Mandatory	The alignment counts for each gene
sampleNames	CSV	Optional	Sample names corresponding the gene counts

Outputs

Name	Type	Description
expr	CSV	Expression data of gene rows and sample columns
log2	LogMatrix	Log2 expression data of gene rows and sample columns

Parameters

Name	Type	Default	Description
add1	boolean	false	Add 1 before doing log2 to avoid negative values.
colIn	string	""	Column name for the original sample names in the annotation file. An empty string refers to the first column.
colOut	string	""	Column name for the intended sample names in the annotation file. An empty string refers to the second column.
counts	boolean	false	Provides the bin counts instead of counts per million mapped fragments.
maxNA	float	1.00	Maximum proportion of missing values accepted for a gene. Genes with more sample values missing are excluded.
normalized	boolean	true	Use robust fpm or normalized counts.

Test cases

Test case	Parameters▼	IN geneCounts	IN sampleNames	OUT expr	OUT log2
case1	properties	geneCounts	sampleNames	expr	(missing)
	counts = true, colIn = alias, colOut = ID

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