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annotate planemo.sh @ 2:46e8eb12f47b draft

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author mmonsoor
date Thu, 17 Dec 2015 09:12:40 -0500
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1 planemo shed_init -f --name=camera_combinexsannos --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html This function check annotations of ion species with the help of a sample from opposite ion mode. As first step it searches for pseudospectra from the positive and the negative sample within a retention time window. For every result the m/z differences between both samples are matched against specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion mode with recalculated annotations. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics"