make_layer function

Creates individual molecular layers from raw data and unique identifiers

Helper function to transform input data to required pipeline input format. Additionally, the supplied input is checked. Allows easy conversion of raw data into the structure accepted by run_pipeline.

make_layer(
  name,
  data_groupA,
  data_groupB,
  identifiers_groupA,
  identifiers_groupB
)

Arguments

• name: [string] Name of the layer.
• data_groupA, data_groupB: [data.frame] Data frame containing raw molecular data of each group (each stratum). Analyzed components (e.g. genes) in columns, samples (e.g. patients) in rows.
• identifiers_groupA, identifiers_groupB: [data.frame] Data frame containing component identifiers (columns) of each component (rows) in the same order as the molecular data frame of each group. These identifiers are used to (a) interconnect graphs and (b) match drugs to drug targets. Must contain a column type which identifies the nature of the component (e.g., "protein")

Returns

Named list containing the supplied data for each group (i.e., the data set for one layer), that can be supplied to run_pipeline and name giving the name of the layer. Each sub-list contains the data and the identifiers.

Examples

data(protein_data)

example_protein_layer <- make_layer(
                             name="protein",
                             data_groupA=protein_data$groupA[, c(-1,-2)],
                             data_groupB=protein_data$groupB[, c(-1,-2)],
                             identifiers_groupA=data.frame(
                                 gene_name=protein_data$groupA$gene_name,
                                 ref_seq=protein_data$groupA$ref_seq),
                             identifiers_groupB=data.frame(
                                 gene_name=protein_data$groupB$gene_name,
                                 ref_seq=protein_data$groupB$ref_seq))