Up: Component summary
Up: Component summary
Function
ExprTableReport
Generates expression statistics into an HTML report. All heatmaps use gene names, so they need to be provided either in a GTF file or as part of the expression matrix. The annotation file can be used also to subset the genes of interest, only genes included in the annotation file will be used for the statistics and plots.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Expression |
| Authors | Alejandra Cervera (alejandra.cervera@helsinki.fi), Katherine Icay (katherine.icay@helsinki.fi), Julia Casado (julia.casado@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| expr | CSV | Mandatory | Expression matrix. Values should be in log2 if visualization is enabled. |
| ref | CSV | Mandatory | CSV file containing sample names and treatment groups. Sample names must match column names of expr. |
| colLabels | CSV | Optional | Label heatmaps with, i.e. clinical information. |
| annotation | GTF | Optional | Ensembl GTF annotation file to be used for grouping genes in biotypes. |
| geneSet | CSV | Optional | One-column list of interesting genes (Ensembl geneId) to create heatmap for. If empty, the oncogenes from the cancer census list will be used. |
| bodyMap | CSV | Optional | Index matrix of geneIds (rows) per tissue (columns). If empty, the Illumina Body Map will be used. |
Outputs| Name | Type | Description |
|---|---|---|
| table | CSV | |
| expressed | CSV | Expression table that has at least one column with the gene or transcript ids, and expression columns corresponding to several samples with the expression values in log2. |
| document | Latex | Document containing all the visuals produced. |
| report | HTML | Expression statistics report. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| bodySite | string | "body" | Any body tissue from the Illumina Body Map, can be the emtpy string or heart, stomach, brain ... |
| keyCol | string | "gene_id" | Column name with the unique ids to be used. |
| minimum | float | 0 | Threshold for minimum expression to be included in the reduced CSV output. |
| nameCol | string | "gene_name" | When input annotation is not provided, then the column containing gene names must be defined from expr. |
| sampleKeyCol | string | "Key" | Column name for sample IDs in input CSV ref. |
| top | int | 10 | Number of top genes to be reported. |
Test cases| Test case | Parameters▼ | IN expr |
IN ref |
IN colLabels |
IN annotation |
IN geneSet |
IN bodyMap |
OUT table |
OUT expressed |
OUT document |
OUT report |
|---|---|---|---|---|---|---|---|---|---|---|---|
| case1 | (missing) | expr | ref | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) | (missing) |