enrichment | R Documentation |
Are selected genes enriched in pathway?
enrichment(
object,
pathwaydt,
fit = fits(object)[1],
coef = coefs(object, fit = fit)[1],
var = abstractvar(object, fit = fit, coef = coef),
levels = fdt(object)[[var]] %>% base::levels() %>% extract(-1),
genevar = "gene",
genesep = "[ ,;]",
n = 3,
verbose = TRUE,
genes = FALSE
)
object |
|
pathwaydt |
pathway |
fit |
string |
coef |
string |
var |
selection fvar |
levels |
selection levels |
genevar |
gene fvar |
genesep |
gene separator (string) |
n |
number |
verbose |
whether to msg |
genes |
whether to report genes |
Four enrichment analyses per geneset using the Fisher Exact Test (see four pvalues). Results are returned in a data.table
in | : genes in pathway |
in.det | : detected genes in pathway |
in.sel | : up/downregulated genes in pathway |
in.up(.genes) | : upregulated genes in pathway |
in.down(.genes) | : downregulated genes in pathway |
out | : genes outside pathway |
det | : detected genes (in + out) |
sel | : up/downregulated genes (in + out) |
up | : upregulated genes (in + out) |
down | : downregulated genes (in + out) |
p.coef.upDET | : prob to randomly select this many (or more) upregulated genes (among detected genes) |
p.coef.downDET | : prob to randomly select this many (or more) downregulated genes (among detected genes) |
p.coef.selDET | : prob to randomly select this many (or more) up OR downregulated genes (among detected genes) |
p.coef.selGEN | : prob to randomly select this many (or more) up OR downregulated genes (among genome genes) |
p.detGEN | : prob to randomly select this many (or more) detected genes (among genome genes) |
# Read
pathwaydt <- read_msigdt(collections = 'C5:GO:BP')
file <- system.file('extdata/atkin.somascan.adat', package = 'autonomics')
object <- read_somascan(file, fit = 'limma', coefs = 't1-t0')
fvars(object) %<>% gsub('EntrezGeneSymbol', 'gene', .)
object %<>% abstract_fit()
var <- abstractvar(object)
varlevels <- c('flat', 'down', 'up')
enrichdt1 <- enrichment(object, pathwaydt, var = var) # 2:n factor
enrichdt2 <- enrichment(object, pathwaydt, var = var, levels = varlevels) # 1:n factor
enrichdt3 <- altenrich(object, pathwaydt) # alternative implementation
cols <- intersect(names(enrichdt1), names(enrichdt3))
all(enrichdt1[, cols, with = FALSE] == enrichdt3[, cols, with = FALSE]) # identical
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