extract_or_convert_gene_ids: Extract Gene IDs from FeatureData or Convert from Probes
In jeffreyLbrabec/tinker: Tissue Network Knowledge Transfer

Description Usage Arguments Value Examples

View source: R/extract_and_convert_gene_ids.R

Extract Gene IDs from FeatureData or Convert from Probes

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extract_or_convert_gene_ids(gse_ESet = NULL, data_species = NULL,
  target_namespace = NULL, convert_to_species = NULL,
  numeric_ns = "")

`gse_ESet`	ExpressionSet S4 object.
`data_species`	A string stating the species of your sequenced data e.g. "hsapiens".
`target_namespace`	The namespace you'd like your probe set to be converted to. A comprehensive list can be found on the gProfileR online tool under the g:Convert tab.
`convert_to_species`	This option is only passed if you need to convert your probeset or gene symbols to another species for downstream analysis. Ignore if no conversion is necessary.
`numeric_ns`	Your probes are from a specific probe set and identifying that probeset helps gconvert know how to convert the probes properly. A list of probe sets properly formatted for gconvert can be found on the gProfileR webpage under the g:Convert tab.

gene_symb a list of gene symbols corresponding to the rows of your expression data

gse <- download_gse_data("GSE108000")

gene_symb <- extract_or_convert_gene_ids(gse, data_species = "hsapiens", 
                                         target_namespace = "ENTREZGENE",
                                         numeric_ns = "AFFY_HUEX_1_0_ST_V2")