Mercurial > repos > proteore > filter_keywords_values
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author | proteore |
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date | Fri, 01 Jun 2018 11:10:47 -0400 |
parents | c6ba1e6f6869 |
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1 Wrapper for Filter by keywords or numerical values Tool | 1 Wrapper for Filter by keywords or numerical values Tool |
2 ======================================================= | 2 ======================================================= |
3 | 3 |
4 **Authors** | 4 **Authors** |
5 | 5 |
6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | 6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
7 | 7 |
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform | 8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform |
9 | 9 |
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | 10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
11 | 11 |
13 | 13 |
14 ------------------------------------------------------- | 14 ------------------------------------------------------- |
15 | 15 |
16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). | 16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). |
17 | 17 |
18 **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** | 18 **Filter by keyword(s)** |
19 | |
20 **Filter the file by keywords** | |
21 | 19 |
22 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. | 20 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. |
23 | 21 |
24 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 | 22 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 |
25 | 23 |
43 | 41 |
44 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. | 42 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. |
45 | 43 |
46 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. | 44 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. |
47 | 45 |
48 **Filter the file by values** | 46 ------------------------------------------------------- |
49 | 47 |
50 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). | 48 **Filter by values** |
51 | 49 |
52 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. | 50 You can filter your data by a column of numerical values. |
51 Enter the column to be use and select one operator in the list : | |
52 | |
53 - "=" | |
54 - "!=" | |
55 - "<" | |
56 - "<=" | |
57 - ">" | |
58 - ">=" | |
59 | |
60 Then enter the value to filter and specify the column to apply that option. | |
61 If a row contains a value that correspond to your settings, it will be filtered. | |
62 | |
63 ------------------------------------------------------- | |
64 | |
65 **Filter by a range of values** | |
66 | |
67 You can also set a range of values to filter your file. | |
68 In opposition to value filter, rows with values inside of the defined range are kept. | |
69 | |
70 Rows with values outside of the defined range will be filtered. | |
71 | |
72 ------------------------------------------------------- | |
73 | |
74 **AND/OR operator** | |
75 | |
76 Since you can add as many filters as you want, you can choose how filters apply on your data. | |
77 | |
78 AND or OR operator option works on all filters : | |
79 | |
80 - OR : only one filter to be satisfied to remove one row | |
81 - AND : all filters must be satisfied to remove one row | |
82 | |
83 ------------------------------------------------------- | |
84 | |
85 **Sort the results files** | |
86 | |
87 You can sort the result file if you wish, it can help you to check results. | |
88 | |
89 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. | |
90 | |
91 Rows stay intact, just in different order like excel. | |
92 You can also choose ascending or descending order, by default descending order is set. | |
93 | |
94 ------------------------------------------------------- | |
53 | 95 |
54 **Output** | 96 **Output** |
55 | 97 |
56 The tool will produce 2 output files. | 98 The tool will produce 2 output files. |
57 | 99 |