Get differentially expressed genes

Differential expression analysis wrapper for presto::wilcoxauc(). Option to return differentially-expressed gene list (return.list = T) or statistics only (return.list = F)

getDEG(
  object,
  assay = DefaultAssay(object),
  data = "data",
  group_by = "seurat_clusters",
  auc.thresh = 0.6,
  fdr.thresh = 0.01,
  logFC.thresh = NA,
  pct.dif.thresh = NA,
  pct.in.thresh = NA,
  pct.out.thresh = NA,
  return.list = F,
  return.all = F,
  sig.figs = NA,
  verbose = T
)

Arguments

object

Seurat object

assay

assay. Default "SCT".

data

data slot. Default "data".

group_by

Name of grouping variable (must be present in object's meta.data)

auc.thresh

AUC threshold. Default = 0.6.

fdr.thresh

FDR threshold. Default = 0.01.

logFC.thresh

logFC threshold. Default = NA.

pct.dif.thresh

Difference in expression percentage. Default = NA.

pct.in.thresh

Expression percentages exceeding this threshold are retained. Default is NA.

pct.out.thresh

Expression percentages below this threshold are retained Default is NA.

return.list

If TRUE, return list of differentially expressed genes. If FALSE, returns table with statistics from differential expression analysis.

return.all

If TRUE, all thresholding filters are ignored, and all results are returned.

sig.figs

If specified and return.list = F, rounds statistics to specified significant figure (recommended: 3). Default is NA.

verbose

Print progress. Default is TRUE.

Value

data.frame or list. Statistics in data.frame output include:

  • avgExpr: Average expression for group

  • logFC: Log fold change

  • statistics: Test statistics

  • auc: Area under curve

  • pval: p-value

  • padj: adjusted p-value

  • pct_in: percentage of expressing cells within group

  • pct_out: percentage of expression cells outside of group

  • pct.dif: difference between pct_in and pct_out

  • sensitivity: pct_in/100

  • specificity: (100-pct_out)/100

  • PPV: positive predictive value

  • NPV: negative predictive value

  • ss: sensitivity x specificity

See also

wilcoxauc

Author

Nicholas Mikolajewicz