diff.analyses.limma

Allows for the computation of differential analyses using limma. Includes means, Fold Changes, and p-values.

# S3 method for class 'analyses.limma'
diff(
  DEprot.object,
  contrast.list,
  include.rep.model = FALSE,
  replicate.column = NULL,
  linear.FC.th = 2,
  linear.FC.unresp.range = c(1/1.1, 1.1),
  padj.th = 0.05,
  padj.method = "BH",
  fitting.method = "ls",
  up.color = "indianred",
  down.color = "steelblue",
  unresponsive.color = "purple",
  null.color = "gray",
  which.data = "imputed",
  overwrite.analyses = FALSE
)

Arguments

DEprot.object

An object of class DEprot.

contrast.list

List of 3-elements vectors indicating (in order): metadata_column, variable_1, variable_2.

replicate.column

String indicating the name of a column from the metadata table in which are stored the replicate IDs. This column is used only if paired.test = TRUE. Default: NULL.

linear.FC.th

Number indicating the (absolute) fold change threshold (linear scale) to use to define differential proteins. Default: 2.

linear.FC.unresp.range

A numeric 2-elements vector indicating the range (linear scale) used to define the unresponsive fold changes. Default: c(1/1.1, 1.1).

padj.th

Numeric value indicating the p.adjusted threshold to apply to the differential analyses. Default: 0.05.

padj.method

String indicating the method to use to correct the p-values. One among: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default: BH.

fitting.method

String indicating the method that limma should use to fit the model. Options: "ls" for least squares or "robust" for robust regression. Default: "ls" (least squares).

up.color

String indicating the color to use for up-regulated proteins in the plots. Default: "indianred".

down.color

String indicating the color to use for up-regulated proteins in the plots. Default: "steelblue".

unresponsive.color

String indicating the color to use for unresponsive proteins in the plots. Default: "purple".

null.color

String indicating the color to use for null proteins in the plots. Default: "gray".

which.data

String indicating which type of counts should be used. One among: 'raw', 'normalized', 'norm', 'imputed', 'imp'. Default: "imputed".

overwrite.analyses

Logical value to indicate whether overwrite analyses already generated. Default: FALSE.