sagetagbyrstat: Find SAGE Tags that are differentially expressed across 2 or...

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

Description

<p>Find SAGE Tags with evidence of differential expression by choosing libraries (more than one) to compare across. A large R value indicates differential expression.

Stekel DJ, Git Y, Falciani F. <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=11116099">The comparison of gene expression from multiple cDNA libraries.</a> Genome Res. 2000. Dec:10(12):2055-61. </p> <p>See the related <a href="showQuestion.do?questionFullName=GeneQuestions.GenesBySageTagRStat"><b>Genes by Differential Expression of SAGE Tag Evidence</b></a> query for summing SAGE tag counts within predicted genes. </p>

Arguments

sage_tag_library_name	Click the + to select specific experiments or use the tree box to select all for the chosen organism. Provide one or more values. Use comma as a delimter.
sage_tag_min_r	Choose a minimum R value to be returned. Stekel et al.???s R-statistic (Stekel, Git, and Falciani 2000) scores SAGE tags on differential expression among libraries (more variable tags have higher R values), with no assignment of significance values.
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

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