DEprot.outliers class

DEprot.outliers class

Slots

metrics

data.frame collecting, for each sample, the three quality metrics, their robust Z-scores/p-values, the individual flags, the total number of flags and the final outlier call, merged with the metadata table. Class: "ANY".

outliers

vector containing the samples called as outliers. Class: "ANY".

sample.subset

vector containing the list of samples analyzed. Class: "ANY".

data.used

vector indicating the type of counts used (imputed, normalized, raw). Class: "ANY".

correlation.method

String indicating the method used for the correlation (e.g., 'pearson', 'spearman', 'kendall'). Class: "ANY".

correlation.matrix

the sample-by-sample correlation matrix used to compute the median correlations, with the diagonal set to NA. Class: "ANY".

PCA

the DEprot.PCA object generated internally and used to compute the Mahalanobis distances. Class: "ANY".

missingness.data.used

vector indicating the type of counts used to quantify the missing values, NA when no unimputed table was available. Class: "ANY".

group.column

String indicating the metadata column used to restrict the correlations to the replicates of the same group, NULL when all the samples were used. Class: "ANY".

metrics.available

logical vector indicating which of the three metrics could effectively be computed. Class: "ANY".

parameters

list of the thresholds used to flag the samples. Class: "ANY".

plot

patchwork object combining the diagnostic plots of all the metrics available. Class: "ANY".

plot.list

list of the individual ggplot objects, one per metric. Class: "ANY".