DEprot.analyses class
metadata
:The data.frame corresponding to the metadata table describing the samples. Class: "ANY"
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raw.counts
:Numeric matrix (rows: proteins, columns: samples) of the raw counts. Class: "ANY"
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norm.counts
:Numeric matrix (rows: proteins, columns: samples) of the normalized counts. Class: "ANY"
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imputed.counts
:Numeric matrix (rows: proteins, columns: samples) of the imputed counts. Class: "ANY"
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log.base
:Numeric value indicating the base of the logarithm expressing the values in the loaded data. Class: "ANY"
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log.transformed
:Logical value indicating whether the data are log-transformed or not. Class: "logical"
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imputed
:Logical value indicating whether the data are imputed. Class: "logical"
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imputation
:String (or any other class) value indicating the imputation method. Class: "ANY"
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normalized
:Logical value indicating whether the data are normalized. Class: "logical"
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normalization.method
:String (or any other class) value indicating the normalization method. Class: "ANY"
. Class: "ANY"
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boxplot.raw
:Ggplot object showing the distribution of the raw values per sample. Class: "ANY"
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boxplot.norm
:Ggplot object showing the distribution of the normalized values per sample. Class: "ANY"
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boxplot.imputed
:Ggplot object showing the distribution of the imputed values per sample. Class: "ANY"
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analyses.result.list
:List containing the differential results for each contrast. Class: "ANY"
. The list contains the following elements:
results
a data.frame containing the results of the analyses; includes average expression of each group, basemean, foldchange, pvalue and p.adj, differential.status
n.diff
a summary table showing the number of proteins in each differential expression status (up/down/unresponsive, null)
PCA.data
output of perform.PCA for the subset of samples analyzed in a specific contrast
PCA.plots
combination of 3 plots: scatter PC1-vs-PC2, scatter PC2-vs-PC3, and cumulative bar plot
correlations
combination of Pearson and Spearman correlation heatmaps (obtained by plot.correlation.heatmap) for the subset of samples analyzed in a specific contrast
volcano
volcano plot showing the log2(FoldChange) x -log10(p.adjusted) of differential expression results; it can be regenerated using plot.volcano
MA.plot
MA-plot showing the log2(basemean) x log2(FoldChange) of differential expression results; it can be regenerated using plot.MA
contrasts
:List of contrasts. each contrast is a vector indicating, in the order: metadata.table.column - groupA - groupB; (groupA / group B). Class: "ANY"
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differential.analyses.params
:List of parameters used to run the differential analyses (fold change thresholds, p-value threshold, p-adjustement method, etc.). Class: "ANY"
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