The function takes as input a list of DFrame and a table with
additional annotations. The annotation tables is automatically
merged into all tables of the list by matching the specified
columns (given by the arguments by and by2). This function is
useful to add annotation to analysis results generated by
scpVarianceAnalysis(), scpDifferentialAnalysis(), or
scpComponentAnalysis(). The annotation table is typically the
colData or rowData of the object used for modelling. In case
of shared column names between the input tables and the annotation
table, any annotation that is already present in the list of
tables will be overwritten by the new annotations.
scpAnnotateResults(tableList, annotations, by, by2 = NULL)A list of tables, typically the output of
scpVarianceAnalysis(), scpDifferentialAnalysis(), or the
the bySample or byFeature elements returned by
scpComponentAnalysis().
A table of class 'data.frame' or 'DFrame' containing the annotations to add. If no further arguments are provided, the table must have row names.
A character(1) providing the name of the column in the
tables in tableList to use to match the rows of the
annotation table.
A character(1) providing the name of the column in the
annotation table to use to match the rows of the tables in
tableList. If NULL, it will be defined by by. The column
pointed by by2 will be dropped in the output tables.
data("leduc_minimal")
var <- scpVarianceAnalysis(leduc_minimal)
colnames(var$Residuals)
#> [1] "feature" "SS" "df"
#> [4] "percentExplainedVar"
## Add peptide annotations available from the rowData
var <- scpAnnotateResults(
var, rowData(leduc_minimal), by = "feature", by2 = "Sequence"
)
colnames(var$Residuals)
#> [1] "feature" "SS"
#> [3] "df" "percentExplainedVar"
#> [5] "Reverse" "Potential.contaminant"
#> [7] "Leading.razor.protein.id" "Leading.razor.protein.symbol"
#> [9] "gene"