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SelCorr |
| Input | |
| SelTag data | Input file in seltag format |
| Fields select |
List of fields -
List of expression fields (tissues) used to calculate correlation between gene expression profiles,
namely field indices in data format of input file starting from 1 (column numeration is not depend on
the Case Names option).
Examples of input: 1;2;3-7;12; 1-12; Fields list - Filename for fields selection in XML format. This is another way to set the list of fields. |
| Genes for select | Genes for select
- List of genes to calculate correlation, namely gene indices in data set of input file starting from 1
(column numeration is not depend on the Case Names option).
Examples of input: 1;2;3-7;12; 1-12; Gene list - Filename for genes selection in XML format for Gene List 1. This is another way to set the list of genes. |
| Genes for comparison | Genes for comparison
- List of genes to which calculate correlation, namely gene indices in data set of input file starting from 1
(column numeration is not depend on the Case Names option).
Examples of input: 1;2;3-7;12; 1-12; Gene list - Filename for genes selection in XML format for Gene List 2. This is another way to set the list of genes. |
| Output | |
| Result | Name of output file |
| Correlation matrix | Output correlation matrix for selected genes |
| XML data | Name of the file for graphical output of correlation coefficient value profiles. If not specified then no graph output assumed. |
| Title | User-specified title of the graph plot. |
| Author | User-specified name of the graph author. |
| Comment | User-specified graph additional commentary line. |
| X axis name | User-specified graph X axis name. |
| Y axis name | User-specified graph Y axis name. |
| Gene selection file | Selected genes can be additionally saved in XML file to be used further by MQSelTag. This parameter specify the name of the output selection file. |
| Name | Name of output selection. |
| Comment | Commentary for the output selection. |
| Options | |
| Type of correlation | Type of correlation coefficient. Three types of correlations are possible: Pearson's r, Spearman rank correlation and Kendall tau correlation. |
| Selection regime |
Regime to treat multiple genes to compare with single gene. Several options are possible:
Max. correlation value to select - the maximal correlation value between expression profiles in gene set to query gene is evaluated; Aver. correlation value to select - average correlation coefficient value is calculated; Corr. for aver field values to select - mean expression values are calculated in the set of genes and their correlation for the query expression profile is calculated. |
| Correlation threshold type | Type of threshold to select best correlating gene pairs. Several options are possible: Best N correlations ; Best % correlations; Correlation coefficient value; Select all pairs. |
| Correlation threshold value | Threshold to select genes from List 1 on the basis of the their correlation coefficient value to genes from List 2. |
| Missing data treatment | Option to treat missing data. Several options are possible : Substitute by means (missing data are substituted by expression means in corresponding field); Case-wise deletion (correlations/distances are calculated by excluding cases that have missing data for any of the selected variables, all correlations are based on the same set of data); Pair-wise deletion (correlations/distances between each pair of profiles are calculated from all fields/samples having valid data for those two profiles). |