Eqmr-fexp

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Introduction

The eqmr-fexp program makes it possible to extract the expression matrix for a given feature database either in binary format to be used by eqmr-expca, or in text format for performing additional analyses with other tools.


Options

Short Long Description
-d --data The database (.db file)
-f --feature The feature database (.fdb file)
-o --output The output file
-t --feature-table A table of features: only those features will be extracted
--qnorm Use this flag to quantile normalize the feature phenotypes within each population
--center Use this flag to center the feature phenotypes within each population
--text Use this flag to get a text file rather than the default binary file


Examples

Let’s extract the whole feature expression matrix in binary format:

$ eqmr-fexp -d data.db -f genes.fdb -o gene_exp_levels.exp

The resulting expression matrix is stored as a binary file, gene_exp_levels.exp, which can be reused for subsequent analyses with eQTNMiner.

However, if we want the same expression matrix but in text format, we just have to use the --text flag as follows:

$ eqmr-fexp -d data.db -f genes.fdb -o gene_exp_levels.txt --text

The file gene_exp_levels.txt is organized as follows: the features are in rows and the samples in columns (the first line provides the name of the samples). Each row starts with the feature name, then come the expression levels for that feature. Missing values are encoded by "NA" (Non Available).



See Also

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Facts about Eqmr-fexpRDF feed
Main source filewarning.png"{{{mainsourcefile}}}" cannot be used as a page name in this wiki.
Program categoryData Management  +
Program languageC  +
Program nameeqmr-fexp  +
Program titleExtract the feature phenotype matrix
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