twoclassdeseq2: Run two class comparison

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Two class differential expression analysis using DESeq2 algorithm.

Usage

twoclassdeseq2(
  moic.res = NULL,
  countsTable = NULL,
  prefix = NULL,
  overwt = FALSE,
  sort.p = TRUE,
  verbose = TRUE,
  res.path = getwd()
)

Arguments

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.

Value

Several .txt files storing differential expression analysis results by DESeq2

References

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.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.