twoclassedger: Run two class comparison
In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description Usage Arguments Details Value References Examples

Two class differential expression analysis using edgeR algorithm.

twoclassedger(
  moic.res = NULL,
  countsTable = NULL,
  prefix = NULL,
  overwt = FALSE,
  sort.p = TRUE,
  verbose = TRUE,
  res.path = getwd()
)

`moic.res`	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
`countsTable`	A matrix of RNA-Seq raw count data with rows for genes and columns for samples.
`prefix`	A string value to indicate the prefix of output file.
`overwt`	A logic value to indicate if to overwrite existing results; FALSE by default.
`sort.p`	A logic value to indicate if to sort adjusted p value for output table; TRUE by default.
`verbose`	A logic value to indicate if to only output id, log2fc, pvalue, and padj; TRUE by default.
`res.path`	A string value to indicate the path for saving the results.

twoclassedger

Several .txt files storing differential expression analysis results by edgeR

Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1):139-140.

McCarthy DJ, Chen Y, Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40(10):4288-4297.