processTarget: Function for pre-processing drug-protein affinity dataset

In Huber-group-EMBL/DepInfeR: Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Function for pre-processing drug-protein affinity dataset

Description

This function is used to preprocess the drug-protein affinity dataset including the following steps: - log-transform kd values (KdAsInput = TRUE) - arctan-transform log(kd) values (KdAsInput = TRUE) - check target similarity and remove highly correlated proteins (removeCorrelated = TRUE) - specify targets that should be kept in the matrix (keepTargets = NULL)

Usage

processTarget(
  targetsMat,
  KdAsInput = TRUE,
  removeCorrelated = TRUE,
  keepTargets = NULL,
  cutoff = 0.8
)

Arguments

targetsMat	Drug-protein affinity matrix with kd values (or optionally other affinity measurement values at roughly normal distribution). Each row is a drug and each column is a sample (cell line or tumor sample).
KdAsInput	A boolean value indicating whether the drug-protein affinity matrix contains kd values which should be log- and arctan-transformed. The default value is TRUE.
removeCorrelated	A boolean value indicating whether highly correlated proteins should be summarized in target groups. The default value is TRUE.
keepTargets	A character variable that specifies important proteins that should be retained in the matrix.
cutoff	A Cosine similarity cutoff value for clustering proteins into one target group. The value should be between 0 and 1.

Details

All steps within this function are optional depending on input data. The transformation steps should be performed if the affinity matrix consists of kd values. If there are highly correlated features within the affinity matrix, they can be removed using the provided function.

Value

A list of two elements: 1)targetMatrix Pre-processed drug-protein affinity matrix; 2)targetCluster, a list that contains the targets show high correlations with each other.

Examples

data(targetMatrix)
processTarget(targetsMat = targetMatrix, KdAsInput = TRUE , removeCorrelated = TRUE)

Huber-group-EMBL/DepInfeR documentation built on April 7, 2023, 7:40 a.m.