Correlation of the standard desviation and the mean of the abundance of a set of genes. — degMV • DEGreport

# Correlation of the standard desviation and the mean of the abundance of a set of genes.

`degMV.Rd`

Correlation of the standard desviation and the mean of the abundance of a set of genes.

    degMV(group, pvalues, counts, sign = 0.01)

## Arguments

group | Character vector with group name for each sample in the same order than counts column names.
pvalues | pvalues of DEG analysis.
counts | Matrix with counts for each samples and each gene.
sign | Defining the cutoff to label significant features. row number should be the same length than pvalues vector.

## 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)
    degMV(colData(dds)[["group"]],
          res[, 4],
          counts(dds, normalized = TRUE))#> Warning: Removed 1 rows containing non-finite values (stat_quantile).#> Warning: Computation failed in `stat_quantile()`:
    #> Package `quantreg` required for `stat_quantile`.
    #> Please install and try again.