create_custom_rna_input_object: Create a generic RNA-seq based input object
In ddeweerd/MODifieRDev: MODifieRDev

Description Usage Arguments Details Value Author(s) See Also

Create a generic RNA-seq based input object

create_custom_rna_input_object(diff_genes = NULL,
  edgeR_deg_table = NULL, annotated_exprs_matrix = NULL,
  count_matrix = 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
`edgeR_deg_table`	A data.frame from `edgeR glmQLFit`
`annotated_exprs_matrix`	A matrix where the rows are genes and the columns samples, used for WGCNA-based methods
`count_matrix`	Matrix containing raw RNA-seq counts
`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 RNA-seq based input object with the same class as objects created by create_input_rna. 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, given that they are provided as arguments to function first:

`diff_genes`	A 2 two column data.frame where the first column are genes and the second column unadjusted p-values
`edgeR_deg_table`	A data.frame from `edgeR glmQLFit`
`annotated_exprs_matrix`	A matrix where the rows are genes and the columns samples. Probes have been collapsed into genes using `collapse_method`
`count_matrix`	A matrix, the original input expression matrix
`group_indici`	A named list containing 2 numeric vectors. The names are the group labels and the values are the group indici