Title: | An Investigation Across Different Species and Tissues |
---|---|
Description: | Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison. |
Authors: | Anisha Haldar [aut] , Vishal H. Oza [aut] , Amanda D. Clark [cre, aut] , Nathaniel S. DeVoss [aut] , Brittany N. Lasseigne [aut] |
Maintainer: | Amanda D. Clark <[email protected]> |
License: | MIT + file LICENSE |
Version: | 1.5.4 |
Built: | 2024-10-26 03:27:26 UTC |
Source: | https://github.com/bioc/CoSIA |
This Class is used to specify the information needed to conduct analysis using CoSIA's other methods. An object of this class will pass as an argument to other methods in CoSIA
CoSIAn object
gene_set
character. A singular gene or a list of genes.
i_species
character. The species corresponding to gene_set.
input_id
character. The type of id corresponding to gene_set.
o_species
character. The singular or list of species that the gene set is being converted to.
output_ids
character. The singular or list of id types that the gene set is being converted to.
mapping_tool
character. The mapping tool, BiomaRt or annotationDBI, being used to map the conversion between IDs.
ortholog_database
character. The ortholog database, HomoloGene or NCBIOrtho, being used to map the conversion between species.
converted_id
data frame. Output of getConversion.
map_tissues
character. A list of tissues being investigated.
map_species
character. A list of species being investigated.
gex
data frame. Output of gene expression data.
metric_type
character. A list of possible metric the user wants to calculate.
metric
data frame. Output of coefficient of variation of gene expression data.
The CoSIAn
constructor creates a CoSIAn
object
from character vector(s).
CoSIAn( gene_set, i_species, input_id, o_species, output_ids, mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues, map_species, metric_type )
CoSIAn( gene_set, i_species, input_id, o_species, output_ids, mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues, map_species, metric_type )
gene_set |
A singular gene or a list of genes. |
i_species |
The species corresponding to gene_set. |
input_id |
The type of id corresponding to gene_set. |
o_species |
The singular or list of species that the gene set is being converted to. |
output_ids |
The singular or list of id types that the gene set is being converted to. |
mapping_tool |
The mapping tool, BiomaRt or annotationDBI, being used to map the conversion between IDs. |
ortholog_database |
The ortholog database, HomoloGene or NCBIOrtho, being used to map the conversion between species. |
map_tissues |
A list of tissues being investigated |
map_species |
A list of species being investigated |
metric_type |
A list of possible metric the user wants to calculate. |
An S4 CoSIAn
object with character vector(s) as slots.
Kidney_Genes <- CoSIAn( gene_set = c( "ENSG00000008710", "ENSG00000118762", "ENSG00000152217" ), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" )
Kidney_Genes <- CoSIAn( gene_set = c( "ENSG00000008710", "ENSG00000118762", "ENSG00000152217" ), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" )
getConversion Generic
getConversion(object)
getConversion(object)
object |
CoSIAn object with all user accessible slots filled |
initializes a generic function for getConversion as preparation for defining the getConversion Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
getConversion Method
## S4 method for signature 'CoSIAn' getConversion(object)
## S4 method for signature 'CoSIAn' getConversion(object)
object |
CoSIAn object with all user accessible slots filled |
CoSIAn object with converted_id slot filled
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
getGEx Generic
getGEx(object)
getGEx(object)
object |
CoSIAn object with all user accessible slots filled with converted_id slot filled |
initializes a generic function for getGEx as preparation for defining the getGEx Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
getGEx Method
## S4 method for signature 'CoSIAn' getGEx(object)
## S4 method for signature 'CoSIAn' getGEx(object)
object |
CoSIAn object with all user accessible slots filled with converted_id slot filled |
CoSIAn Object with gex slot filled
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
getGExMetrics Generic
getGExMetrics(object)
getGExMetrics(object)
object |
CoSIAn object with all user accessible slots filled with converted_id slot filled |
initializes a generic function for getGExMetrics as preparation for defining the getGExMetrics Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
getGExMetrics Method
## S4 method for signature 'CoSIAn' getGExMetrics(object)
## S4 method for signature 'CoSIAn' getGExMetrics(object)
object |
CoSIAn object with all user accessible slots filled with converted_id slot filled |
CoSIAn Object with metric slot filled
Kohl M (2022). MKdescr: Descriptive Statistics. R package version 0.8, https://github.com/stamats/MKdescr.
Zhang JD, Hatje K, Sturm G, Broger C, Ebeling M, Burtin M, Terzi F, Pomposiello SI, Badi L (2017). “Detect tissue heterogeneity in gene expression data with BioQC.” BMC Genomics, 18(1), 277. http://accio.github.io/BioQC/.
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("r_norvegicus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
getTissues
getTissues(species)
getTissues(species)
species |
name of a species or multiple species that you want to get available tissue list for |
list of tissues that are common/available among the species or multiple species inputted
tissue <- getTissues(c("m_musculus"))
tissue <- getTissues(c("m_musculus"))
plotCVGEx Generic
plotCVGEx(object)
plotCVGEx(object)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled |
initializes a generic function for plotCVGEx as preparation for defining the plotCVGEx Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = c("adult mammalian kidney","heart"), map_species = c("h_sapiens", "r_norvegicus"), metric_type = "CV_Tissue" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plot <- plotCVGEx(Kidney_gene_metric)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = c("adult mammalian kidney","heart"), map_species = c("h_sapiens", "r_norvegicus"), metric_type = "CV_Tissue" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plot <- plotCVGEx(Kidney_gene_metric)
plotCVGEx Method
## S4 method for signature 'CoSIAn' plotCVGEx(object)
## S4 method for signature 'CoSIAn' plotCVGEx(object)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled |
plot object
Dot plot in R with the dotchart function [with examples]. R CODER. (2020, November 20). Retrieved from https://r-coder.com/dot-plot-r/
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = c("adult mammalian kidney","heart"), map_species = c("h_sapiens", "r_norvegicus"), metric_type = "CV_Tissue" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plot <- plotCVGEx(Kidney_gene_metric)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "h_sapiens", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = c("adult mammalian kidney","heart"), map_species = c("h_sapiens", "r_norvegicus"), metric_type = "CV_Tissue" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plot <- plotCVGEx(Kidney_gene_metric)
plotDSGEx Generic
plotDSGEx(object)
plotDSGEx(object)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled |
initializes a generic function for plotDSGEx as preparation for defining the plotDSGEx Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plotDSGEx(Kidney_gene_metric)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plotDSGEx(Kidney_gene_metric)
plotDSGEx Method
## S4 method for signature 'CoSIAn' plotDSGEx(object)
## S4 method for signature 'CoSIAn' plotDSGEx(object)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled |
plot object
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plotDSGEx(Kidney_gene_metric)
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion) plotDSGEx(Kidney_gene_metric)
plotSpeciesGEx Generic
plotSpeciesGEx(object, single_tissue, single_gene)
plotSpeciesGEx(object, single_tissue, single_gene)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled |
single_tissue |
one tissue that the user wants to investigate across the mapped species |
single_gene |
one ensembl id that the user wants to investigate across the mapped species |
initializes a generic function for plotSpeciesGEx as preparation for defining the plotSpeciesGEx Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")
plotSpeciesGEx Method
## S4 method for signature 'CoSIAn' plotSpeciesGEx(object, single_tissue, single_gene)
## S4 method for signature 'CoSIAn' plotSpeciesGEx(object, single_tissue, single_gene)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled |
single_tissue |
one tissue that the user wants to investigate across the mapped species |
single_gene |
one ensembl id that the user wants to investigate across the mapped species |
plot object
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")
plotTissueGEx Generic
plotTissueGEx(object, single_species, single_gene)
plotTissueGEx(object, single_species, single_gene)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled |
single_species |
one species that the user wants to investigate across the mapped tissues |
single_gene |
one ensembl id that the user wants to investigate across the mapped tissues |
initializes a generic function for plotTissueGEx as preparation for defining the plotTissueGEx Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")
plotTissueGEx Method
## S4 method for signature 'CoSIAn' plotTissueGEx(object, single_species, single_gene)
## S4 method for signature 'CoSIAn' plotTissueGEx(object, single_species, single_gene)
object |
CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled |
single_species |
one species that the user wants to investigate across the mapped tissues |
single_gene |
one ensembl id that the user wants to investigate across the mapped tissues |
plot object
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("m_musculus"), metric_type = "DS_Gene" ) Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes) Kidney_gene_gex <- getGEx(Kidney_gene_conversion) plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")
viewCoSIAn Generics
viewCoSIAn(object, slot_name)
viewCoSIAn(object, slot_name)
object |
CoSIAn object with all user accessible slots filled |
slot_name |
name of output slots |
initializes a generic function for viewCoSIAn as preparation for defining the viewCoSIAn Method
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("d_melanogaster"), metric_type = "DS_Gene" ) viewCoSIAn(Kidney_Genes, "converted_id")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("d_melanogaster"), metric_type = "DS_Gene" ) viewCoSIAn(Kidney_Genes, "converted_id")
viewCoSIAn
## S4 method for signature 'CoSIAn' viewCoSIAn(object, slot_name)
## S4 method for signature 'CoSIAn' viewCoSIAn(object, slot_name)
object |
CoSIAn object with all user accessible slots filled |
slot_name |
name of output slots |
slots in CoSIAn object
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("d_melanogaster"), metric_type = "DS_Gene" ) viewCoSIAn(Kidney_Genes, "converted_id")
Kidney_Genes <- CoSIAn( gene_set = c("ENSG00000008710", "ENSG00000152217"), i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c( "d_melanogaster" ), output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI", ortholog_database = "HomoloGene", map_tissues = "heart", map_species = c("d_melanogaster"), metric_type = "DS_Gene" ) viewCoSIAn(Kidney_Genes, "converted_id")