getResultsNames: Inference the name of results of DESeq analysis by a formula...

In WTaoUMC/RegEnrich: Gene regulator enrichment analysis

Description

Inference the name of results of DESeq analysis by a formula (or model matrix) and sample information

Usage

getResultsNames(design, pData = NULL)

Arguments

design	either a formula or a model matrix.
pData	a data frame, showing the information of each sample. If design is a formula, the pData must be include the columns that identical to the terms of the design formula. If design is a model matrix, then pData is not used. Default is NULL.

Value

the names of contrast parameter (list of character format) that regenrich_diffExpr and results function can use, and it is the same as the value that resultsNames function returns.

Examples

# formula with intercept
design = ~condition
pData = data.frame(condition = factor(c('A', 'A', 'A', 'B', 'B', 'B'),
                                      c('A', 'B')))
getResultsNames(design, pData)

# formula without intercept
design = ~0+condition
getResultsNames(design, pData)

# formula with two terms
design = ~condition+treatment
pData = data.frame(condition = factor(rep(c('A', 'B'), each= 4),
                                      c('A', 'B')),
                   treatment = factor(rep_len(c('Ctrl', 'Treat'), 8),
                                      c('Ctrl', 'Treat')))
getResultsNames(design, pData)

# formula with two terms and an interaction term
design = ~condition+treatment+condition:treatment
getResultsNames(design, pData)

# design is a model matrix
pData = data.frame(condition = factor(rep(c('A', 'B'), each= 4),
                                      c('A', 'B')),
                   treatment = factor(rep_len(c('Ctrl', 'Treat'), 8),
                                      c('Ctrl', 'Treat')))
design = model.matrix(~condition+treatment, pData)
getResultsNames(design)

WTaoUMC/RegEnrich documentation built on Aug. 4, 2021, 4:11 p.m.