Description Usage Arguments Value Author(s) See Also Examples
View source: R/summary.goglm.R
Summerize GOglm results (from the goglm
function)
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x |
An object of class |
en.cut |
P-value cut-off for declaring enriched categories (default = 0.05) |
... |
Other parameters (for future use) |
Some descriptive summaries based on the goglm
result
Gu Mi mig@stat.oregonstate.edu, Yanming Di diy@stat.oregonstate.edu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Load the datasets into R session:
data(ProsCan_DE)
DE_data <- ProsCan_DE
data(ProsCan_Length)
Length_data <- ProsCan_Length
## Prepare a data frame to be passed to goglm():
gene_table <- prepare(DE_data, Length_data, trans.p = "d.log", trans.l = TRUE)
## For illustration, only consider a subset of genes:
gene_data <- gene_table[1:100,1:2]
## Prepare the "category-to-genes" list:
library(goseq)
gene2cats <- getgo(rownames(gene_data), "hg18", "ensGene")
cat2genes <- revMap(gene2cats)
## Run goglm():
res <- goglm(gene_data, cat2genes, n=5)
names(res) # "GOID" "over.p" "anno" "rank"
## For a summary of the GOglm results:
summary(res)
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