Up: Component summary
Up: Component summary
Component
EdgeRComputes the digital expression fold change and p-value based on counts. The counts are normalized before fold change is calculated. Only the unpaired samples test is implemented.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | edgeR (R-bioconductor) |
| Source files | component.xml EdgeR.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| counts | CSV | Mandatory | A matrix of read counts for gene, transcript or other tracked genomic feature (rows) in the sample set (columns). Rows with missing values are ignored. |
| groups | SampleGroupTable | Mandatory | Sample groups for counts input columns. |
| reads | CSV | Optional | Total number of reads for each sample in counts. If reads is not set, the sum of counts for each sample is used instead. |
Outputs| Name | Type | Description |
|---|---|---|
| logratio | CSV | Logratios computed based on target and reference groups. The overall concentration of a tag, p-value for logratios and, if correction was used, the corrected p-values are also included for each row in the input. |
| plot | Latex | MA plot of pvalue dispersion with the top 500 genes highlighted. |
| normalized | CSV | Normalized counts per tag. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| correction | string | "fdr" | Method for multiple hypothesis correction of exact test p-values. One of 'none' (no correction), 'fdr' (default), 'robustfdr', 'BY', 'holm' or 'bonferroni'. |
| dispersion | string | "tag" | Sets dispersion method for exact test. One of 'tag' (tagwise) or 'common'. |
| normMethod | string | "TMM" | Method for normalization of counts. One of 'TMM', 'RLE' or 'upperquartile'. |
| normQuartile | float | 0.75 | Quartile for scaling factor in quartile normalization. Only used when normMethod='quartile'. |
| onlyNorm | boolean | false | Only normalize counts. |
| pLimitPlot | float | 0.05 | P-Value threshold for defining a differentially expressed gene. Only used for dispersion plot output. |
| referenceGroup | string | "" | Name of reference group in groups input. Only used if normMethod='TMM'. If referenceGroup is empty, the sample with an upper quartile closest to the mean upper quartile is used as reference. |
| targetGroup | string | (no default) | Name of target (case) group in groups input. Only used if normMethod='TMM'. |
Test cases| Test case | Parameters▼ | IN counts |
IN groups |
IN reads |
OUT logratio |
OUT plot |
OUT normalized |
|---|---|---|---|---|---|---|---|
| case1 | properties | counts | groups | reads | logratio | plot | (missing) |
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referenceGroup = G2, |
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| case2 | properties | counts | groups | (missing) | logratio | (missing) | (missing) |
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referenceGroup = G2, |
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| case3_emptyCounts | properties | counts | groups | reads | (expecting failure) | (expecting failure) | (expecting failure) |
|
targetGroup = G1 |
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| case4_onecol | properties | counts | groups | (missing) | logratio | (missing) | normalized |
|
referenceGroup = G2, |
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| case5_onlyCounts | properties | counts | groups | reads | (missing) | (missing) | normalized |
|
referenceGroup = G2, |
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