mdgsa (version 1.4.2)

uvPat: Uni-Variate Gene Set Analysis Pattern Classification.

Description

Classifies significant patterns form a Uni-Variate Gene Set Analysis.

Usage

uvPat(gsaout, cutoff = 0.05, pvalue = "padj", statistic = "lor")

Arguments

gsaout

data.frame; output from uvGsa.

cutoff

p-value cutoff for considering significant a Gene Set.

pvalue

p-value column to be used. Default is named "padj" as in uvGsa output.

statistic

name of the column containing the log odds ratio from the uvGsa analysis.

Value

• A numeric vector (values: -1, 0, 1) indicating relationship between the Gene Set and the ranking variable: [object Object],[object Object],[object Object]

Details

Sign of the 'lor' and p-value are used to define functional blocks as up-regulated, down-regulated or not enriched.

See Also

uvGsa, mdPat

Examples

uvGsa.res <- as.data.frame (list (N    = c (10, 20, 30, 40),
                                  lor  = c (1.45, -0.32, 1.89, -1.66),
                                  pval = c (0.001, 0.002, 0.05, 0.06)))
uvGsa.res[,"padj"] <- p.adjust (uvGsa.res$pval, "BY")
uvGsa.res

uvGsa.res[,"pat"] <- uvPat (uvGsa.res)
uvGsa.res