results {NBAMSeq} | R Documentation |
This function pulls out result from NBAMSeqDataSet object
returned by NBAMSeq
results(object, name, contrast, indepfilter = TRUE, alpha = 0.1, pAdjustMethod = "BH", parallel = FALSE, BPPARAM = bpparam(), ...)
object |
a NBAMSeqDataSet object returned by |
name |
the name of nonlinear variable or continuous linear variable |
contrast |
a character of length 3. 1st element: name of factor variable; 2nd element: name of numerator level; 3rd element: name of denominator level. contrast = c("group", "treatment", "control") means comparing treatment vs control for group variable. |
indepfilter |
either TRUE or FALSE indicating whether independent filtering should be performed. Default is TRUE. |
alpha |
significant threhold for declaring genes as differentially expressed. Default is 0.1. |
pAdjustMethod |
pvalue adjustment method. Default is "BH". See
|
parallel |
either TRUE or FALSE indicating whether parallel should be used. Default is FALSE. |
BPPARAM |
|
... |
additional arguments provided to |
a DataFrame which contains the result
Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15:550. https://doi.org/10.1186/s13059-014-0550-8
gsd = makeExample(n = 3, m = 10) gsd = NBAMSeq(gsd) res = results(gsd, name = "pheno")