genesbymicroarrpagetbrucei: Identify T.brucei genes based on fold change...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description Arguments Value

Find genes based on fold change expression difference between a "comparison" lifecycle stage and a reference lifecycle. Whole genome comparison of RNA levels for both protein coding genes and structural RNAs in five different life cycle stages: in vivo slender bloodstream form, in vivo stumpy bloodstream form, cultured bloodstream form, log-phase procyclic culture form and stationary-phase procyclic culture form. RNA from three independent biological replicates from five different life cycle stages were hybridized to Nimblegen arrays (Madison,WI USA) that contained 8 probes per open reading frame and 3 probes per structural RNA spotted three times per array. For this experiment, in the cases where the probe set mapped to near-identical genes, data was assigned to a single representative gene. (see Jensen et al. PMID: 19840382.)

`life_cyc_brucei_ref`	Choose a life cycle stage
`life_cyc_brucei_cmp`	Choose a life cycle stage
`fold_change`	Enter a non-negative number. NOTE: Fold change is reported in the summary as positive numbers for up-regulated genes and negative numbers for down-regulated genes
`regulated_dir`	For ConditionA vs. ConditionB, select up-regulated for genes where ConditionA > ConditionB and select down-regulated for genes where ConditionB > ConditionA.
`confidence`	PaGE reports 1 - False Discovery Rate (FDR), which is called the "confidence" for the predictions. The FDR of a set of predictions is the expected percent of false predictions in the set of predictions. For example if the algorithm returns 100 genes with a false discovery rate of .3 (confidence=0.7) then we should expect 70 of them to be correct.
`protein_coding_only`	Should only protein coding genes be returned?
`o-fields`	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`o-tables`	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`.convert`	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and `TRUE`, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is `FALSE`, the value from the Web server is returned as is.
`.url`	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
`.json`	a logical value controlling whether to use the JSON or the XML version of the method