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updated README
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sigven committed Feb 7, 2021
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Expand Up @@ -131,14 +131,14 @@ _oncoEnrichR_ works in two basic steps through the following two methods:
Argument |Description
------------- |----------------
```query``` | character vector with gene/query identifiers
```query_id_type``` | character indicating source of query (one of 'uniprot_acc', 'symbol', 'entrezgene', or 'ensembl_gene_id')
```query_id_type``` | character indicating type of identifier used for query set (one of 'uniprot_acc', 'symbol', 'entrezgene', or 'ensembl_gene_id')
```ignore_id_err``` | logical indicating if analysis should continue when erroneous/unmatched query identifiers are encountered in query or background gene set
```project_title``` | project title (report title)
```project_owner``` | project owner (e.g. lab/PI)
```project_description``` | brief description of project, how target list was derived
```bgset``` | character vector with gene identifiers, used as reference/background for enrichment/over-representation analysis
```bgset_id_type``` | character indicating source of background ('uniprot_acc','symbol','entrezgene','ensembl_gene_id')
```bgset_description``` | character indicating type of background (e.g. 'All lipid-binding proteins (n = 200)')
```bgset_id_type``` | character indicating type of identifier used for background set ('uniprot_acc','symbol','entrezgene','ensembl_gene_id')
```bgset_description``` | character with description of background gene set (e.g. 'All lipid-binding proteins (n = 200)')
```p_value_cutoff_enrichment``` | cutoff p-value for enrichment/over-representation analysis
```p_value_adjustment_method``` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
```q_value_cutoff_enrichment``` | cutoff q-value for enrichment analysis
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