Up: Component summary
Up: Component summary
Function
DiffExprSeqFor differential expression at gene and exon level of RNA-Seq data. You can use HTSeqBam2Counts to prepare the suitable inputs for this function.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Alejandra Cervera (alejandra.cervera@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
| Deprecated |
The exon part is outdated, and the standard case is the same as DEan. |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| exonCounts | Array<BinaryFile> | Optional | The alignment counts for each exon |
| geneCounts | Array<BinaryFile> | Optional | The alignment counts for each gene |
| annotation | GFF | Optional | Provides the gene annotations in GFF format. These files can be obtained from a GTF annotation file using HTSeqBam2Counts function. |
| conditions | CSV | Optional | A csv with at least one column named Condition with the conditions to be tested. The list should be in the same order as the count files in the input arrays. If defined then conditionList parameter is ignored. |
Outputs| Name | Type | Description |
|---|---|---|
| exon | CSV | Table with the results of the exon level analysis |
| gene | CSV | Table with the results of the gene level analysis |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| conditionList | string | "A,A,B,B" | A comma separated list of conditions to be tested for differential expression in the same order as the samples. Example: conditionA,conditionA,conditionB,conditionB |
| level | string | "Exon" | Level at which the differential expression is obtained. Possible values "Exon,Gene", "Exon" or "Gene". |
| minCount | int | 5 | Minimum number of reads covering the exon to be considered. |
| nCores | int | 5 | Number of threads for the analysis |
Test cases| Test case | Parameters▼ | IN exonCounts |
IN geneCounts |
IN annotation |
IN conditions |
OUT exon |
OUT gene |
|---|---|---|---|---|---|---|---|
| case1_exon | properties | exonCounts | (missing) | annotation | (missing) | (missing) | (missing) |
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# For testing DiffExprSeq, |
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| case2_gene | properties | (missing) | geneCounts | (missing) | conditions | (missing) | (missing) |
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# For testing DiffExprSeq, |
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