test_classification_celllines: DrugPrediction TESTING version 1

In patterja/kbmtl: KBMTL Drug Prediction

Description

DrugPrediction TESTING version 1

Usage

test_classification_celllines(combined_matrix, train_idx, test_idx,
  cell_line_response = "cell_line_response_threshold_0.50_large_and_small_screen.RData",
  targetid = "target_id.txt", genelist = "Trusight_genes.csv", state)

Arguments

combined_matrix	(string):path to FINAL_norm.txt run through normalizeRUV in SMMARTFunctions.R
train_idx	(string):cell_line_response_threshold_0.50_large_and_small_screen.RData
test_idx	(string):cell_line_response_threshold_0.50_large_and_small_screen.RData
cell_line_response	(string): cell_line_response_threshold_0.50_large_and_small_screen.RData. Cell line are rows and drugs are columns.
targetid	(string): path to target_id.txt. Converts to HUGO identifiers and filters to protein coding genes.
genelist	(string): path to gene list Trusight.csv. Used to filter genes associated with cancer. Make sure gene identifiers match.
state	(string): path to "smmart_trained_machine_learning_model.RData" from drugPredTrain

Value

Y_predicted(data.frame): prediction

Author(s)

Janice Patterson

patterja/kbmtl documentation built on Oct. 6, 2020, 1:16 p.m.