Mercurial > repos > proteore > filter_keywords_values
diff README.rst @ 7:6f32c1e12572 draft default tip
planemo upload commit 72b345a7df2c87f07a9df71ecee1f252c9355337
author | proteore |
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date | Fri, 01 Jun 2018 11:10:47 -0400 |
parents | c6ba1e6f6869 |
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--- a/README.rst Fri Apr 20 09:07:23 2018 -0400 +++ b/README.rst Fri Jun 01 11:10:47 2018 -0400 @@ -3,7 +3,7 @@ **Authors** -T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform @@ -15,9 +15,7 @@ This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). -**For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output** - -**Filter the file by keywords** +**Filter by keyword(s)** Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. @@ -45,11 +43,55 @@ **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. -**Filter the file by values** +------------------------------------------------------- + +**Filter by values** + +You can filter your data by a column of numerical values. +Enter the column to be use and select one operator in the list : + +- "=" +- "!=" +- "<" +- "<=" +- ">" +- ">=" + +Then enter the value to filter and specify the column to apply that option. +If a row contains a value that correspond to your settings, it will be filtered. + +------------------------------------------------------- + +**Filter by a range of values** + +You can also set a range of values to filter your file. +In opposition to value filter, rows with values inside of the defined range are kept. -You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). +Rows with values outside of the defined range will be filtered. + +------------------------------------------------------- + +**AND/OR operator** + +Since you can add as many filters as you want, you can choose how filters apply on your data. + +AND or OR operator option works on all filters : + +- OR : only one filter to be satisfied to remove one row +- AND : all filters must be satisfied to remove one row -* For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. +------------------------------------------------------- + +**Sort the results files** + +You can sort the result file if you wish, it can help you to check results. + +In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. + +Rows stay intact, just in different order like excel. +You can also choose ascending or descending order, by default descending order is set. + +------------------------------------------------------- **Output**