The expand module is the first analysis step in the metaQuantome analysis workflow, and can be run to analyze function, taxonomy, or function and taxonomy together.
To prepare to run this module, you must create your samples file with "metaQuantome: create samples file" and download the necessary databases with "metaQuantome: database".
Some example analysis workflows are:
The following information is required for all 3 analysis modes (function, taxonomy, and function-taxonomy).
In function mode, the following information is required:
In taxonomy mode, the following information is required:
In the combined mode, all of the above must be provided. In addition, the "target rank" must be provided, which is the desired taxonomic rank at which to summarize the function/taxonomy results.
The structure of the output file depends on the analysis mode and the experimental design, but the columns generally look like this, with one row for each term:
term id | info about term. (one or more columns) | mean term intensity (by sample group) | term intensity (by sample) | number of unique peptides (by sample) | number of sample children in each sample |
---|---|---|---|---|---|
term1 | name, rank, etc. | note that this is the log2 of the mean intensity | this is the log2 of term intensity in each sample. Missing data is coded as NA. | integer. 0 is coded as NA | integer. 0 is coded as NA |
The next step in the metaQuantome workflow is "filter", which filters out rows that don't meet certain conditions on the intensity, the number of unique peptides annotated with each term, and the number of sample children.
Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.