Distribution of the standard desviation of DE genes compared to the background

Distribution of the standard desviation of DE genes compared to the background

degVB(tags, group, counts, pop = 400)

Arguments

tags	List of genes that are DE.
group	Character vector with group name for each sample in the same order than counts column names.
counts	matrix with counts for each samples and each gene. Should be same length than pvalues vector.
pop	Number of random samples taken for background comparison.

Value

ggplot2 object

Examples

data(humanGender)
library(DESeq2)
idx <- c(1:10, 75:85)
dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
  colData(humanGender)[idx,], design=~group)
dds <- DESeq(dds)
#> using pre-existing size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> -- replacing outliers and refitting for 1 genes
#> -- DESeq argument 'minReplicatesForReplace' = 7 
#> -- original counts are preserved in counts(dds)
#> estimating dispersions
#> fitting model and testing
res <- results(dds)
degVB(row.names(res)[1:20], colData(dds)[["group"]],
  counts(dds, normalized = TRUE))