significants: Method to get the significant genes

In lpantano/DEGreport: Report of DEG analysis

Method to get the significant genes

Description

Function to get the features that are significant according to some thresholds from a DEGSet, DESeq2::DESeqResults and edgeR::topTags.

Usage

significants(object, padj = 0.05, fc = 0, direction = NULL, full = FALSE, ...)

## S4 method for signature 'DEGSet'
significants(object, padj = 0.05, fc = 0, direction = NULL, full = FALSE, ...)

## S4 method for signature 'DESeqResults'
significants(object, padj = 0.05, fc = 0, direction = NULL, full = FALSE, ...)

## S4 method for signature 'TopTags'
significants(object, padj = 0.05, fc = 0, direction = NULL, full = FALSE, ...)

## S4 method for signature 'list'
significants(
  object,
  padj = 0.05,
  fc = 0,
  direction = NULL,
  full = FALSE,
  newFDR = FALSE,
  ...
)

Arguments

object	DEGSet
padj	Cutoff for the FDR column.
fc	Cutoff for the log2FC column.
direction	Whether to take down/up/ignore. Valid arguments are down, up and NULL.
full	Whether to return full table or not.
...	Passed to deg. Default: value = NULL. Value can be 'raw', 'shrunken'.
newFDR	Whether to recalculate the FDR or not. See https://support.bioconductor.org/p/104059/#104072. Only used when a list is giving to the method.

Value

a dplyr::tbl_df data frame. gene column has the feature name. In the case of using this method with the results from degComps, log2FoldChange has the higher foldChange from the comparisons, and padj has the padj associated to the previous column. Then, there is two columns for each comparison, one for the log2FoldChange and another for the padj.

Author(s)

Lorena Pantano

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD=1)
colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12)
  design(dds) <-  ~ condition + treatment
dds <- DESeq(dds)
res <- degComps(dds, contrast = list("treatment_B_vs_A",
                                     c("condition", "A", "B")))
significants(res, full = TRUE)
# significants(res, full = TRUE, padj = 1) # all genes

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