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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

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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