enrichANAT: Method to enrich in anatomical terms provided by Bgee...

In isglobal-brge/postRexposome: Package to enrich exposome-omic data analyis results.

Description

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Usage

enrichANAT(object, rid = 1, fData.tag = 1, sel.pval = c("P.Value",
  "adj.P.Val"), th.pval = 0.01, sel.feature = "genes", feature.null = "",
  bgee.data = c("rna_seq", "affymetrix", "est", "in_situ"),
  statistic = "fisher", verbose = FALSE, warnings = TRUE)

Arguments

object	Object of class ResultSet.
rid	(default 1) If given ResultSet hat has more than one result, id to select the result where the enrichment will be performed.
fData.tag	(default 1) Identifier of the annotation to be used to mach the probes of ResultSet with gene identifier. In other words, index of the element in fData that matches the omic dataset to be used in the enrichment.
sel.pval	(default "adj.P.Val") Name of the P.Value columns to filter datset's probes given th.pval.
th.pval	(default 0.01) Threshold used to include a probe (CpG) into the enrichment analysis.
sel.feature	(default "genes") Name containing gene identifier in ResultSet's fData.
feature.null	(default "") String identifier for non gene-assigned probes.
bgee.data	(default "affymetrix") Type of data requested to Bgee to perform the functinal enrichment. Can take any of them or more than one of the possibles options.
statistic	(default "fisher") Statistic used to test the enrichment in Bgee anatomical categories throught topGO R package. Check whichTests() for available tests.
verbose	(default FALSE) If set to TRUE messages indicating the steps done by the method are raised.
warnings	(default TRUE) If set to FALSE important notes raised by the method are hide.

Note

Komljenovic A, Roux J, Robinson-Rechavi M, Bastian F; BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests. F1000Research (2016).

Bastian F, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M; Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species; Data Integration Life Sci. Lecture Notes in Computer Science (2008)

isglobal-brge/postRexposome documentation built on May 18, 2019, 5:50 a.m.