Up: Component summary
Up: Component summary
Component
SummariseSummarises values for different rows of a file (i.e. reference) according to the clustered and possibly filtered result of the file (i.e. clusterFiles). A column should be assigned to row IDs of the reference file. This is to keep the track of possible filterings in the clusterFiles.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Ali Oghabian (ali.oghabian@helsinki.fi) |
| Requires | R |
| Source files | component.xml Summarise.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| clusterFiles | CSVList | Mandatory | Filtered files directory. A column should be assigned to the row id numbers according to the original Pre-filtered data (i.e. reference parameter). An additional column should also be aassigned to the cluster numbers of the rows (i.e. Event IDs in flow cytometry analysis). clusterFiles should have the same names as the reference files. |
| reference | CSVList | Mandatory | The reference CSV files. The Compensated data-table is recomended in flow cytometry analysis. A column should be assigned to the row id numbers (e.g. Event IDs in flow cytometry analysis). If the summaries are required to be calculated for the clustered files, the same link as the clusterFiles could be assigned to reference. |
Outputs| Name | Type | Description |
|---|---|---|
| summaries | CSVList | csv files including the summary tables i.e. summary values for each cluster of the files. each row represents a cluster number which could be accessed through "cluster" column and other clusters include the summary calculations of the related columns in the rows grouped in similar clusters. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| clusterCol | string | "cluster" | The name of the column in the clusterFiles which represents the cluster number of the rows. |
| culsterIDCol | string | "Event" | The name of the column in the clusterFiles which represents the Row IDs, row names or the Event numbers of the cells in flow cytometry analysis. |
| referenceIDCol | string | "Event" | The name of the column in the reference files which represents the Row IDs, row names or the Event numbers of the cells in the flow cytometry analysis. |
| summaryType | string | "mean" | The summary type of interest. Three types of mean, median, and var are available. |
Test cases| Test case | Parameters▼ | IN clusterFiles |
IN reference |
OUT summaries |
||
|---|---|---|---|---|---|---|
| case1 | properties | clusterFiles | reference | summaries | ||
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summaryType=mean |
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