Description Usage Arguments Value See Also Examples
View source: R/reactomepa.enrich.R
reactome.enrich utilizes the package 'ReactomePA' to test for enrichment of reactome pathways in your gene list
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CSS |
output CRISPR screen score matrix from create.CSS() |
genome.db |
genome database from which to convert gene symbols to entrez ids |
pvalue |
specified cutoff for pathway significance (default = 0.05) |
combine |
logical: do you want to combine the columns in the data? (default=FALSE) |
combine.by |
vector separating the columns of your data into groups for comparing multiple groups |
metric |
defines whether to look for enrichment based on a gene list of differentially expressed genes defined by a 'cutoff' (default) or by 'gsea' (one sample or fully combined samples only) |
cutoff |
numeric cutoff to define differential expression (default = 1) |
save |
logical: saves plots to pdf |
save.table |
logical: saves tables of enriched pathways |
showCategory |
number of categories to display |
font.size |
font size of labels in dotplot and barplot |
list of (1) output from ReactomePA enrichment tests and (2) readable output
1 2 3 4 5 | reactome.enrich <- reactomepa.enrich(CSS.data[,1, drop=FALSE])
reactome.enrich <- reactomepa.enrich(CSS.data[,c(1:5)])
reactome.enrich <- reactomepa.enrich(CSS.data[,c(1:5)], combine = T)
reactome.enrich <- reactomepa.enrich(CSS.data[,1, drop = FALSE], metric = 'gsea')
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