subDEG: limma/voom differential gene expression analysis

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Description

Wrapper function to perform eBayes differential gene expression analysis (DEG).

Usage

subDEG(
  emat,
  class,
  batch = NULL,
  keepN = TRUE,
  doPairwise = FALSE,
  doVoom = FALSE,
  normMethod = "quantile",
  returnTreat = FALSE,
  lfc = log2(1.5),
  padj = 0.05,
  feat = NULL,
  doPlot = FALSE,
  sortBy = "P",
  ...
)

Arguments

emat	numeric matrix with row features and sample columns. For ExpressionSet exprs matrix is used and featureData used for annotating results.
class	a factor vector specifying subtypes compared. length(class)==ncol(emat).
batch	a factor vector specifying additional level in design matrix.
keepN	a logical or numeric vector specifying which samples to keep (defaults to all).
doPairwise	a logical, whether pairwise comparison are to be performed (as opposed to class k against K-k).
doVoom	a logical, indicating whether emat is sequencing count data.
normMethod	a character, only used if doVoom=TRUE and passed to
returnTreat	logical, if true, parameters lfc and padj are passed to topTreat, else eBayes are used and results sorted as indicated by sortBy parameter.
lfc	numeric, only applicable if returnTreat=TRUE, if FALSE, all genes are returned
padj	numeric, only applicable if returnTreat=TRUE, if FALSE, all genes are returned
feat	data frame with feature data
doPlot	a logical, not implemented.
sortBy	character passed to topTable sort.by parameter.
...	additional arguments passed to calcNormFactors calcNormFactors if element in c("TMM","RLE", "upperquartile","none") or voom ("scale", "quantile", "cyclicloess").

Value

a data frame (for two classes) or list of data frames (in case of more than two classes) with results.

References

Wu D, Smyth GK. Camera: a competitive gene set test accounting for inter-gene correlation. Nucl. Acids Res. 2012;gks461. http://nar.oxfordjournals.org/content/early/2012/05/24/nar.gks461

Examples

deg <- subDEG(crcTCGAsubset, crcTCGAsubset$CMS, doVoom=TRUE, sortBy="P")
lapply(deg, head)

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.