twoclasslimma: 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 limma algorithm.

twoclasslimma(
  moic.res = NULL,
  norm.expr = 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.
`norm.expr`	A matrix of normalized expression data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.
`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.

twoclasslimma

Several .txt files storing differential expression analysis results by limma

Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res, 43(7):e47.