Plot main figures showing p-values distribution and mean-variance correlation — degQC • DEGreport
Description: This function joins the output of degMean, degVar and degMV in a single plot. See these functions for further information.

# Plot main figures showing p-values distribution and mean-variance correlation

`degQC.Rd`

This function joins the output of `degMean`, `degVar` and `degMV` in a single plot. See these functions for further information.

    degQC(counts, groups, object = NULL, pvalue = NULL)

## Arguments

counts | Matrix with counts for each samples and each gene.
groups | Character vector with group name for each sample in the same order than counts column names.
object | DEGSet oobject.
pvalue | pvalues of DEG analysis.

## 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)
    degQC(counts(dds, normalized=TRUE), colData(dds)[["group"]],
      pvalue = res[["pvalue"]])