create_custom_microarray_input_object: Create a generic microarray based input object
In ddeweerd/MODifieRDev: MODifieRDev

Description Usage Arguments Details Value Author(s) See Also

Create a generic microarray based input object

create_custom_microarray_input_object(diff_genes = NULL,
  limma_probe_table = NULL, annotated_exprs_matrix = NULL,
  expression_matrix = NULL, annotation_table = NULL,
  group1_indici = NULL, group2_indici = NULL, group1_label = NULL,
  group2_label = NULL, settings = NULL)

`diff_genes`	A 2 two column data.frame where the first column are genes and the second column are p-values
`limma_probe_table`	A data.frame from `limma topTable` with added gene annotation
`annotated_exprs_matrix`	A matrix where the rows are genes and the columns samples.
`expression_matrix`	Normalized expression matrix where the samples are columns and probes are rows
`annotation_table`	A dataframe providing annotation for the probes. The dataframe should have 3 columns: PROBEID: The probe id as it is in the expression matrix IDENTIFIER: The entrez id (if available) associated with the probe
`group1_indici`	vector containing indici for samples belonging to group 1 (Column numbers)
`group2_indici`	vector containing indici for samples belonging to group 2 (Column numbers)
`group1_label`	Label for each group 1, for example "patient" or "control"
`group2_label`	Label for each group 2, for example "patient" or "control"
`settings`	Settings used to generate the object. Used only internally by the package.

This function allows the creation of a generic microarray based input object with the same class as objects created by create_input_microarray. This can be useful in the cases where you already have differentially expressed genes, an annotated expression matrix or both and want to wrap that into an input object to use in downstream analysis. All arguments are optional.

The function returns an object of class "MODifieR_input". The object is a named list containing the following components:

`diff_genes`	A 2 two column data.frame where the first column are genes and the second column p-values
`limma_probe_table`	A data.frame from `limma topTable` with added gene annotation
`annotated_exprs_matrix`	A matrix where the rows are genes and the columns samples. Probes have been collapsed into genes using `collapse_method`
`expression_matrix`	A matrix, the original input expression matrix
`annotation_table`	A data.frame, the original annotation table used to annotate the probes
`group_indici`	A named list containing 2 numeric vectors. The names are the group labels and the values are the group indici