runDEA: Run differential expression analysis
In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description Usage Arguments Details Value References Examples

Using choosen algorithm to run differential expression analysis between two classes identified by multi-omics clustering process.

runDEA(
  dea.method = c("deseq2", "edger", "limma"),
  expr = NULL,
  moic.res = NULL,
  prefix = NULL,
  overwt = FALSE,
  sort.p = TRUE,
  verbose = TRUE,
  res.path = getwd()
)

`dea.method`	A string value to indicate the algorithm for differential expression analysis. Allowed value contains c('deseq2', 'edger', 'limma'). The former two require RNA-Seq raw count data and the last one requires normalized expression data (FPKM or TPM without log2 transformation is recommended).
`expr`	A matrix of expression data.
`moic.res`	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
`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.

runDEA

Several .txt files storing differential expression analysis results by specified algorithm

Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15(12):550-558.

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.

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.