degSummary: Print Summary Statistics of Alpha Level Cutoffs

In lpantano/DEGreport: Report of DEG analysis

Print Summary Statistics of Alpha Level Cutoffs

Description

Print Summary Statistics of Alpha Level Cutoffs

Usage

degSummary(
  object,
  alpha = c(0.1, 0.05, 0.01),
  contrast = NULL,
  caption = "",
  kable = FALSE
)

Arguments

object	Can be DEGSet or DESeqDataSet or DESeqResults.
alpha	Numeric vector of desired alpha cutoffs.
contrast	Character vector to use with results() function.
caption	Character vector to add as caption to the table.
kable	Whether return a knitr::kable() output. Default is data.frame.

Value

data.frame or knitr::kable().

Author(s)

Lorena Pantano

References

• original idea of multiple alpha values and code syntax from Michael Steinbaugh.

Examples

library(DESeq2)
data(humanGender)
idx <- c(1:5, 75:80)
counts <- assays(humanGender)[[1]]
dse <- DESeqDataSetFromMatrix(counts[1:1000, idx],
                              colData(humanGender)[idx,],
                              design = ~group)
dse <- DESeq(dse)
res1 <- results(dse)
res2 <- degComps(dse, contrast = c("group_Male_vs_Female"))
degSummary(dse, contrast = "group_Male_vs_Female")
degSummary(res1)
degSummary(res1, kable = TRUE)
degSummary(res2[[1]])

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.