getResultsNames {RegEnrich} | R Documentation |
Inference the name of results of DESeq analysis by a formula (or model matrix) and sample information
getResultsNames(design, pData = NULL)
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. |
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.
# 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)