genesbymicroarrpagetcruzi: Identify <i>T.cruzi</i> genes based on fold change expression...

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

Find genes based on fold change expression difference between a "comparison" lifecycle stage and a reference lifecycle. <br><br>RNAs from 3 biological replicates from a single time point in each stage were subjected to DNA microarrays containing probes for the complete, annotated T. cruzi genome. <i>T. cruzi</i> lifecycle stages assessed in this study: trypomastigotes, amastigotes, epimastigotes, and metacyclic trypomastigotes. For additional details, refer: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19664227">http://www.ncbi.nlm.nih.gov/pubmed/19664227</a>

Arguments

life_cyc_cruzi_ref	Choose a life cycle stage
life_cyc_cruzi_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

Value

text/xml text/plain

duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.