Summarize DESeq2 results into a dataframe

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

library(DESeq2)

# make example DESeq data set
dds <- makeExampleDESeqDataSet()

# run DESeq2
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing

# make comparisons
res <- results(dds, contrast=c('condition', 'A', 'B'))

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