report_significance: Report significant results

Description Usage Arguments Details Value

Description

Significant results reported as PCA plots and dendrograms

Usage

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report_significance(mat, fit, groups = NULL, coef = colnames(fit$design)[2],
  prefix = coef, invisible = T)

Arguments

mat

matrix used to report the results

fit

fitLM object from limma

groups

a named vector with the classification used to report results

coef

a character with the tested condition to be reported

prefix

character, the file prefix to report the results

invisible

a boolean to determine if the output of 'missMethyl::gometh' is returned

Details

Extracts the significance analysis from a given variable. Features with an adjusted P-value lower or equal to 0.05 are taken as significant and used to summarize the results with PCA plots and hierarchical clustering.

Value

limma::topTable


xpastor/skima documentation built on May 16, 2019, 3:25 p.m.