Up: Component summary
Up: Component summary
Component
GenomeSliderSummarized genomic events at sliding window intervals and/or at predifined regions. The summarizing function can be specified eg. mean, median, sum, max, min. Missing values are handled.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Analysis |
| Authors | Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | GenomicRanges (R-bioconductor) |
| Source files | component.xml GenomeSlider.R |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| matrix | CSV | Mandatory | Input csv file having the data to be summarized. |
| regions | CSV | Optional | Predefined regions for which summarizing will be performed. If not provided, only sliding window will be performed. |
| chrLengths | CSV | Optional | CSV file containing chromosome lengths. Needed only for sliding window summarization. |
Outputs| Name | Type | Description |
|---|---|---|
| regionsSummary | CSV | Summarization over predifined regions. |
| windowsSummary | CSV | Summarization over sliding windows. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| echoRegionColumns | string | "" | Comma-separated column names for the columns from regions input to be echoed in the regionSummary output. If empty (default), no columns will be echoed. |
| func | string | "" | The summarization function can be one of the following: "mean","median","sum","max","min". If empty string (default) was selected, the summarization will count events in matrix that overlaps with predefined regions or windows. |
| matrixCategoryColumn | string | "" | Name of the column that has different categories. The output will have one column for each category in this column with values corresponding to category counts in each genomic region. |
| matrixCollapseColumn | string | "" | Name of the column that has different categories or IDs. The output will have one column having collapsed (comma-separated) unique categories or IDs present in the coresponding genomic region. |
| matrixDataColumns | string | "" | R expression for selecting the data columns in matrix input e.g. "c(1,2,3)", "1:3", "c('column1','column2','column3')". If empty (default), the summarization will count events in matrix that overlaps with predefined regions or windows. |
| matrixRegionColumns | string | "" | Comma-separated column names for the chr-start-end columns in matrix input respectively. If empty (default), first three columns will be considered. |
| regionColumns | string | "" | Comma-separated column names for the chr-start-end columns in regions input respectively. If empty (default), first three columns will be considered. |
| stepSize | int | 0 | Step size for sliding window. If zero (default), non-overlapping windows will be generated. |
| windowSize | int | 1000 | The size of sliding window. |
Test cases| Test case | Parameters▼ | IN matrix |
IN regions |
IN chrLengths |
OUT regionsSummary |
OUT windowsSummary |
|---|---|---|---|---|---|---|
| case1 | properties | matrix | regions | chrLengths | regionsSummary | windowsSummary |
|
windowSize=12, |
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| case2 | properties | matrix | regions | chrLengths | regionsSummary | windowsSummary |
|
windowSize=12, |
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| case3 | properties | matrix | regions | chrLengths | regionsSummary | windowsSummary |
|
windowSize=50, |
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