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Summarize DESeq2 results into a dataframe

Source: R/functions.R
my.summary.Rd

summary(res) prints out info; this function captures it into a dataframe

Usage

my.summary(res, dds, alpha, lfc.thresh = 0)

Arguments

res

DESeq2 results object

dds

DEseq2 object

alpha

Alpha level at which to call significantly changing genes

lfc.thresh

log2FoldChange threshold

Value

Dataframe of summarized results

Examples

n_genes <- 100

#  make mock dds list
dds <- DESeq2::makeExampleDESeqDataSet(n=n_genes)

# make mock results df
res <- data.frame(
         baseMean = runif(n_genes, 10, 1000),
         log2FoldChange = rnorm(n_genes, 0, 2),
         lfcSE = runif(n_genes, 0.1, 0.5),
         stat = rnorm(n_genes, 0, 3),
         pvalue = runif(n_genes, 0, 1),
         padj = runif(n_genes, 0, 1),
         symbol = paste0("GENE", 1:n_genes),
         row.names = paste0("gene", 1:n_genes)
       )

# get summary
df <- my.summary(res, dds, alpha=0.1)