The monolith function that wraps the emrineJ cli. It is recommended to use
the wrapper functions (ora, gsr,
corr, roc).
ermineR(annotation = NULL, aspects = c("Molecular Function", "Cellular Component", "Biological Process"), scores = NULL, hitlist = NULL, scoreColumn = 1, threshold = 0.001, expression = NULL, bigIsBetter = FALSE, customGeneSets = NULL, geneReplicates = c("mean", "best"), logTrans = FALSE, pAdjust = c("FDR", "FWE"), test = c("ORA", "GSR", "CORR", "ROC"), iterations = NULL, stats = c("mean", "quantile", "meanAboveQuantile", "precisionRecall"), quantile = 50, geneSetDescription = "Latest_GO", output = NULL, return = TRUE, minClassSize = 20, maxClassSize = 200)
| annotation | Annotation. A file path, a data.frame or a platform short
name (eg. GPL127). If given a platform short name it will be downloaded
from annotation repository of Pavlidis Lab (www.chibi.ubc.ca/microannots/).
Note that if there is a file or folder with the same name as the platform
name in the directory, that file will be read instead of getting a copy from
Pavlidis Lab. If this file isn't a valid annotation file, the function will fail.
If providing a custom annotation file, see If you are providing a custom gene set, you can leave annotation as NULL |
|---|---|
| aspects | Character vector. Which Go aspects to include in the analysis.
Can be in long form (eg. 'Molecular Function') or short form (eg. |
| scores | A data.frame. Rownames have to be gene identifiers (eg. probes,
must be unique), followed by any number of columns. The column used for
scoring is chosen by |
| scoreColumn | Integer or character. Which column of the |
| threshold | Double. Score threshold (test = ORA only) |
| expression | A file path or a data frame. Expression data. (test = CORR only) Necesary correlation anaylsis. See http://erminej.msl.ubc.ca/help/input-files/gene-expression-profiles/ for data format |
| bigIsBetter | Logical. If TRUE large scores are considered to be higher.
|
| customGeneSets | Path to a directory that contains custom gene set files, paths to custom gene set files themselves or a named list of character strings. Use this option to create your own gene sets. If you provide directory you can specify probes or gene symbols to include in your gene sets. See http://erminej.msl.ubc.ca/help/input-files/gene-sets/ for information about format for this file. If you are providing a list, only gene symbols are accepted. |
| geneReplicates | What to do when genes have multiple scores in input file (due to multiple probes per gene) |
| logTrans | Logical. Should the data be -log10 transformed. Recommended for
p values. |
| pAdjust | Which multiple test correction method to use. Can be "FDR" or 'Westfall-Young' (slower). |
| test | Method for computing gene set significance |
| iterations | Number of iterations. We suggest a starting value of 10000 iterations. When you decide on parameters you like, we recommend a larger number of iterations (perhaps 200,000 or more). This is to get sufficient precision in the p-values to make multiple-test correction work correctly. (test = GSR CORR and precRecall methods only) |
| stats | Method for computing raw class statistics (test = GSR only) |
| quantile | Integer. Quantile to use. (stats = meanAboveQuantile only) |
| geneSetDescription | "Latest_GO", a file path that leads to a GO XML or OBO file or a URL that leads to a go ontology file that ends with rdf-xml.gz. If you left annotation as NULL and provided customGeneSets, this argument is
not required and will default to NULL. Otherwise, by default it'll be set to
"Latest_GO" which downloads the latest available GO XML file. This option won't work
without an internet connection. To get a frozen file
that you can use later, see |
| output | Output file name. |
| return | If results should be returned. Set to FALSE if you only want a file |
| minClassSize | minimum class size |
| maxClassSize | maximum class size |
A list