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HTSeqExprNormalize

Takes as input "raw", integer count expression matrix of quantified sequenced reads and outputs a scale-normalised, log-transformed expression matrix. Developed for the output of htseq-count.

Version 0.1
Bundle sequencing
Categories Normalization
Authors Katherine Icay (katherine.icay@helsinki.fi)
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Requires libxml2-dev (DEB) ; EdgeR (R-bioconductor) ; DESeq (R-bioconductor)
Source files component.xml normalised_exprMatrices.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr CSV Mandatory Expression matrix of raw counts. First column is miRNA/smallRNA IDs. Column headers are sample names. Recommended: output file of HTSeqExprMatrix.

Outputs

Name Type Description
array Array<CSV> Array of scale-normalised, log-transformed expression matrices. Two files for each option parameter are produced: one where log(0) values are replaced with NA to prevent -Inf values, and one where a pseudocount of 1 is added to the entire expression matrix to preserve the profile and ensure log(0+1) is 0.

Parameters

Name Type Default Description
options string "edger" Comma-seperated list of possible scale-normalization methods to use. Possible options are "deseq", "edgeR" and/or "uqnorm". Options are not case-sensitive, but are spelling-sensitive. DESeq = counts scaled by library size (estimateSizeFactors). EdgeR = counts per million. UQnorm = counts scaled by the library's top 25th percentile.

Test cases

Test case Parameters IN
expr
OUT
array
case1 properties expr array

options=edger,deseq, uqNorm


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