View source: R/fct_06_pathway.R
pathway_select_data | R Documentation |
Return a data matrix that is a subset of the processed data and only contains genes that are in the gene set of the desired pathway.
pathway_select_data(
sig_pathways,
gene_sets,
contrast_samples,
data,
select_org,
all_gene_names
)
sig_pathways |
Description of the pathway for which to obtain the gene expression data |
gene_sets |
List of vectors with each vector being the
set of genes that correspond to a particular pathway in
the database. See list returned from
|
contrast_samples |
Vector of sample columns that correspond to the selected comparison |
data |
Matrix of gene data that has been through
|
select_org |
String designating the organism being analyzed |
all_gene_names |
Matrix of all the matched and converted
gene IDs from |
Sub-data matrix from the processed data. Only contains genes from the selected pathway and samples that correspond to the comparison being analyzed.
Other pathway functions:
fgsea_data()
,
find_overlap()
,
gage_data()
,
get_gsva_plot_data()
,
get_pathway_list_data()
,
get_pgsea_plot_all_samples_data()
,
get_pgsea_plot_data()
,
gsva_data()
,
kegg_pathway()
,
pgsea_data()
,
pgsea_plot_all()
,
plot_gsva()
,
plot_pgsea()
,
reactome_data()
,
remove_pathway_id()
,
remove_pathway_id_second()
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