Panther Package
This package suport PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System.
More information in http://pantherdb.org
To install the Panther package, follow the following steps:
- Change to working directory
cd analysis
- Clone the repository
git clone https://github.com/RafaellaFerraz/Panther.git
- Install using install.package
install.packages("~/analysis/Panther/", repos = NULL, type="source")
Given a list of genes and a species, this service return the gene ontology annotations, PANTHER protein class annotations and Reactome pathways.
Parameters:
genes: Genes identifier. Maximum of 1000 Identifiers. Examples: Ensemble gene identifier, Ensemble protein identifier, Ensemble transcript identifier, Entrez gene id, gene symbol, NCBI GI, HGNC Id, International protein index id, NCBI UniGene id, UniProt accession and UniProt id.
organism: Taxon id. Ex.: 9606
data <- panther_map(genes = c("BRCA1", "VDR", "HBB"), organism = "9696")
Return:
name: Pathways' name
id: Gene Ontology ID
panther_id: Annotation id from PANTHER
panther_label: Annotation label from PANTHER
gene_acession: Id of the gene from HGNC and UniProtKB \
Overrepresentation function compares a gene list with a reference gene list, and determines whether a particular class (e.g. molecular function, biological process, cellular component) is overrepresented or underrepresented in input list.
Parameters:
genes: Genes identifier. Maximum of 1000 Identifiers. Examples: Ensemble gene identifier, Ensemble protein identifier, Ensemble transcript identifier, Entrez gene id, gene symbol, NCBI GI, HGNC Id, International protein index id, NCBI UniGene id, UniProt accession andUniProt id
organism: One taxon id required. Ex.: 9606
ref_list: If not specified, the system will use all the genes for the specified organism. Each identifier to be delimited by comma i.e. ','. Maximum of 100000 Identifiers. Examples: Ensemble gene identifier, Ensemble protein identifier, Ensemble transcript identifier, Entrez gene id, gene symbol, NCBI GI, HGNC Id, International protein index id, NCBI UniGene id, UniProt accession andUniProt id
refOrganism: This parameter is only required if parameter 'ref_list' has been specified. Only one taxon id can be specified.
annotDataSet: One of the supported PANTHER annotation data types. Use the 'support_annot' function to retrieve list of supported annotation data types. Ex: GO:0003674
testtype: Fisher's Exact test will be used by default. Options: "FISHER" and "BINOMIAL"
correction: correction of enrichment. Options: "FDR", "BONFERRONI" and "NONE" \
data <- panther_over(genes = c("BRCA1", "VDR", "HBB"), annotDataSet = "GO:0003674")
Return:
number_in_list
fold_enrichment: proportion of term genes found in the input list compared to the. proportion of total term genes found in the background
fdr correction
expected
number_in_reference
pValue
term.id: Gene Ontology ID
term.label
plus_minus
Retrieve the list of supported annotation data sets by PANTHER
sup <- support_annot()
Return:
Returns information about annotation data sets supported by PANTHER
release_date
description
id
label
version