Eqmr-fdb

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Contents

Introduction

The eqmr-fdb program creates a database for the phenotypic features. Several kinds of features are available:

When either an exon, a transcript or a gene has multiple probes inside, there will be a single final expression level per sample. To summarize the expression measurements from multiple probes, eqmr-fdb can use the following methods:

For the exon or metaexon levels, it is also possible to compute specific exon levels by using the two following methods:


Options

Short Long Description
-d --data The database file (.db)
-f --feature Either the feature type or the feature database (.fdb)
-m --method The summarization method for feature with multiple probes
-o --output The output file
-p --min-probe The minimum number of probes (default is 1)
-e --exon-index When -f exon, the method to create the exon index (default is none)
--gene-to-feature Output the gene-feature relationship for a given feature database
--exon-covariate For exon feature database, output details on exon features
--metaexon-covariate For metaexon feature database, output details on exon features
--stats Output Median/MAD of each feature within each population


Examples

$ eqmr-fdb -d data.db -f gene -m median -o data_genexp


Remarks


See Also

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