Distribution of the standard desviation of DE genes compared to the background — degVB • DEGreport

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

`degVB.Rd`

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 testingres <- results(dds)
    degVB(row.names(res)[1:20], colData(dds)[["group"]],
      counts(dds, normalized = TRUE))