From 61738070f393cd03b7cbb6c5e095fe1f815bddf6 Mon Sep 17 00:00:00 2001 From: Julien Wollbrett Date: Fri, 15 Jun 2018 18:52:44 +0200 Subject: [PATCH] update documentation --- man/Bgee-class.Rd | 5 ++--- man/formatData.Rd | 8 +++++--- man/geneList.Rd | 19 +++++++++++++------ man/getAnnotation.Rd | 1 + man/getData.Rd | 1 + man/listBgeeRelease.Rd | 1 + man/listBgeeSpecies.Rd | 1 + man/loadTopAnatData.Rd | 1 + man/makeTable.Rd | 1 + man/topAnat.Rd | 1 + 10 files changed, 27 insertions(+), 12 deletions(-) diff --git a/man/Bgee-class.Rd b/man/Bgee-class.Rd index 2e18fbf..8b7dd6d 100644 --- a/man/Bgee-class.Rd +++ b/man/Bgee-class.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/Bgee.R \docType{class} \name{Bgee-class} -\alias{Bgee-class} \alias{Bgee} +\alias{Bgee-class} \title{Bgee Reference Class} \description{ This is used to specify information at the beginning of a BgeeDB working session, for example, the targeted species and data type. An object of this class is then passed as argument to other functions of the package to provide these informations. See examples in vignette. @@ -33,8 +33,6 @@ By default all data type are included: \code{c("rna_seq","affymetrix","est","in_ \item{\code{quantitativeData}}{A field specifying if a single type of quantitative expression data ("rna_seq" or "affymetrix") was specified and if it is available for targeted species, helping the package to know if it should proceed with the execution of getAnnotation() and getData() functions.} }} - - \examples{ { bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq") @@ -42,3 +40,4 @@ By default all data type are included: \code{c("rna_seq","affymetrix","est","in_ } } + diff --git a/man/formatData.Rd b/man/formatData.Rd index 10543f6..afd62c8 100644 --- a/man/formatData.Rd +++ b/man/formatData.Rd @@ -13,7 +13,8 @@ formatData(myBgeeObject, data, stats = NULL, callType = "all") \item{stats}{A character indicating what expression values should be used in the formatted data expressionSet object matrix. \itemize{ - \item{"rpkm" for RNA-seq} + \item{"rpkm" for RNA-seq (Bgee release 13.2 and before)} + \item{"fpkm" for RNA-seq (Bgee release 14 and above)} \item{"counts" for RNA-seq} \item{"tpm" for RNA-seq (Bgee release 14 and above)} \item{"intensities" for Affymetrix microarrays} @@ -36,13 +37,14 @@ This function formats the data downloaded with the getData() function into an ob { bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq") dataMouseGSE43721 <- getData(bgee, experimentId = "GSE43721") - dataMouseGSE43721.rpkm <- formatData(bgee, + dataMouseGSE43721.fpkm <- formatData(bgee, dataMouseGSE43721, callType = "present", - stats = "rpkm") + stats = "fpkm") } } \author{ Andrea Komljenovic and Julien Roux. } + diff --git a/man/geneList.Rd b/man/geneList.Rd index 524c625..acb2434 100644 --- a/man/geneList.Rd +++ b/man/geneList.Rd @@ -3,18 +3,25 @@ \docType{data} \name{geneList} \alias{geneList} -\title{Example of gene list object used to run a topAnat enrichment test, created on April 18th, 2017. +\title{Example of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a ```topGOdata``` object in the ```topGO``` package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. -In this example the foreground genes are zebrafish genes annotated with "spermatogenesis" in the Gene Ontology (or annotated to children terms of "spermatogenesis"), and the background is composed of all zebrafish genes with at least one Gene Ontology annotation. +In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package.} -\format{A named vector of factor values with 22141 elements. The factor levels are "0" for the 22103 genes in the background and "1" for the 38 genes in the foreground. Vector names are the Ensembl IDs of the zebrafish genes.} +\format{A named vector of factor values with 3005 elements. The factor levels are "0" for the 2858 genes in the background and "1" for the 147 genes in the foreground. Vector names are the Ensembl IDs of the zebrafish genes.} \usage{ -geneList +data(geneList) } \description{ -Example of gene list object used to run a topAnat enrichment test, created on April 18th, 2017. +Example of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a ```topGOdata``` object in the ```topGO``` package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. -In this example the foreground genes are zebrafish genes annotated with "spermatogenesis" in the Gene Ontology (or annotated to children terms of "spermatogenesis"), and the background is composed of all zebrafish genes with at least one Gene Ontology annotation. +In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package. } +\examples{ +bgee <- Bgee$new(species = "Danio_rerio") +myTopAnatData <- loadTopAnatData(bgee) +data(geneList) +myTopAnatObject <- topAnat(myTopAnatData, geneList) +} \keyword{datasets} + diff --git a/man/getAnnotation.Rd b/man/getAnnotation.Rd index 49273ea..c1b40c8 100644 --- a/man/getAnnotation.Rd +++ b/man/getAnnotation.Rd @@ -25,3 +25,4 @@ This function loads the annotation of experiments and samples of quantitative ex \author{ Andrea Komljenovic and Julien Roux. } + diff --git a/man/getData.Rd b/man/getData.Rd index 0e5ace3..7950a69 100644 --- a/man/getData.Rd +++ b/man/getData.Rd @@ -28,3 +28,4 @@ This function loads the quantitative expression data and presence calls for samp \author{ Andrea Komljenovic and Julien Roux. } + diff --git a/man/listBgeeRelease.Rd b/man/listBgeeRelease.Rd index 63ae55a..109e37a 100644 --- a/man/listBgeeRelease.Rd +++ b/man/listBgeeRelease.Rd @@ -24,3 +24,4 @@ Returns information on available Bgee releases, the access URL for FTP and webse \author{ Julien Roux, Julien Wollbrett } + diff --git a/man/listBgeeSpecies.Rd b/man/listBgeeSpecies.Rd index b4d18b0..2499152 100644 --- a/man/listBgeeSpecies.Rd +++ b/man/listBgeeSpecies.Rd @@ -35,3 +35,4 @@ Returns information on available species in Bgee \author{ Julien Roux } + diff --git a/man/loadTopAnatData.Rd b/man/loadTopAnatData.Rd index 4d46a51..1668dad 100644 --- a/man/loadTopAnatData.Rd +++ b/man/loadTopAnatData.Rd @@ -61,3 +61,4 @@ The expression calls come from Bgee (\url{http://bgee.org}), that integrates dif \author{ Julien Roux, Julien Wollbrett } + diff --git a/man/makeTable.Rd b/man/makeTable.Rd index e86feee..729ccb6 100644 --- a/man/makeTable.Rd +++ b/man/makeTable.Rd @@ -73,3 +73,4 @@ fold enrichment and FDR. Data are sorted by p-value and only terms below the spe \author{ Julien Roux } + diff --git a/man/topAnat.Rd b/man/topAnat.Rd index df6c54b..5e81857 100644 --- a/man/topAnat.Rd +++ b/man/topAnat.Rd @@ -70,3 +70,4 @@ To perform the enrichment test for expression in anatomical structures for each \author{ Julien Roux } +