pathfindR (version 1.3.0)

input_processing: Process Input

Description

Process Input

Usage

input_processing(input, p_val_threshold, pin_path, org_dir = NULL,
  human_genes = TRUE)

Arguments

input

the input data that pathfindR uses. The input must be a data frame with three columns:

1. Gene Symbol (HGNC Gene Symbol)

2. Change value, e.g. log(fold change) (Not obligatory)

3. adjusted p value associated with test, e.g. differential expression/methylation

p_val_threshold

the adjusted-p value threshold to use when filtering the input data frame

pin_path

path to the Protein Interaction Network (PIN) file used in the analysis

org_dir

path/to/original/directory, supplied by run_pathfindR (default = NULL)

human_genes

boolean to indicate whether the input genes are human gene symbols or not (default = TRUE)

Value

This function first filters the input so that all p values are less than or equal to the threshold. Next, gene symbols that are not found in the PIN are identified. If aliases of these gene symbols are found in the PIN, the symbols are converted to the corresponding aliases. The resulting data frame containing the original gene symbols, the updated symbols, change values and p values is then returned.

See Also

See run_pathfindR for the wrapper function of the pathfindR workflow

Examples

# NOT RUN {
input_processing(RA_input, 0.05, return_pin_path("KEGG"))
# }
# NOT RUN {
# }