deseq_polar function

Convert DESeq2 objects to a volcano3d object

This function is used instead of polar_coords if you have raw RNA-Seq count data. It takes 2 DESeqDataSet objects, extracts statistical results and converts the results to a 'volc3d' object, which can be directly plotted.

deseq_polar(
  object,
  objectLRT,
  contrast = NULL,
  data = NULL,
  pcutoff = 0.05,
  padj.method = "BH",
  filter_pairwise = TRUE,
  ...
)

Arguments

• object: An object of class 'DESeqDataSet' with the full design formula. The function DESeq needs to have been run.
• objectLRT: An object of class 'DESeqDataSet' with the reduced design formula. The function DESeq needs to have been run on this object with argument test="LRT".
• contrast: Character value specifying column within the metadata stored in the DESeq2 dataset objects is the outcome variable. This column must contain a factor with 3 levels. If not set, the function will select the last term in the design formula of object as per DESeq2 convention.
• data: Optional matrix containing gene expression data. If not supplied, the function will pull the expression data from within the DESeq2 object using the DESeq2 function assay(). NOTE: for consistency with gene expression datasets, genes are in rows.
• pcutoff: Cut-off for p-value significance
• padj.method: Can be any method available in p.adjust or "qvalue". The option "none" is a pass-through.
• filter_pairwise: Logical whether adjusted p-value pairwise statistical tests are only conducted on genes which reach significant adjusted p-value cut-off on the group likelihood ratio test
• ...: Optional arguments passed to polar_coords

Returns

Calls polar_coords to return an S4 'volc3d' object

Examples

library(DESeq2)

  counts <- matrix(rnbinom(n=1500, mu=100, size=1/0.5), ncol=15)
  cond <- factor(rep(1:3, each=5), labels = c('A', 'B', 'C'))

  # object construction
  dds <- DESeqDataSetFromMatrix(counts, DataFrame(cond), ~ cond)

  # standard analysis
  dds <- DESeq(dds)

  # Likelihood ratio test
  ddsLRT <- DESeq(dds, test="LRT", reduced= ~ 1)

  polar <- deseq_polar(dds, ddsLRT, "cond")
  volcano3D(polar)
  radial_ggplot(polar)

See Also

polar_coords, voom_polar, DESeq in the DESeq2 package