Analyze Difference of Drug Response (IC50 Value (uM)) between Gene (Signature) High and Low Expression with CCLE Data

Usage

analyze_gene_drug_response_diff(
  gene_list,
  drug = "ALL",
  tissue = "ALL",
  combine = FALSE,
  cutpoint = c(50, 50)
)

Arguments

gene_list: a gene symbol list.
drug: a drug name. Check examples.
tissue: a tissue name. Check examples.
combine: if TRUE, combine the expression of gene list as a gene signature.
cutpoint: cut point (in percent) for High and Low group, default is c(50, 50).

Value

a data.frame.

Examples

tissue_list <- c(
  "prostate", "central_nervous_system", "urinary_tract", "haematopoietic_and_lymphoid_tissue",
  "kidney", "thyroid", "soft_tissue", "skin", "salivary_gland",
  "ovary", "lung", "bone", "endometrium", "pancreas", "breast",
  "large_intestine", "upper_aerodigestive_tract", "autonomic_ganglia",
  "stomach", "liver", "biliary_tract", "pleura", "oesophagus"
)

drug_list <- c(
  "AEW541", "Nilotinib", "17-AAG", "PHA-665752", "Lapatinib",
  "Nutlin-3", "AZD0530", "PF2341066", "L-685458", "ZD-6474", "Panobinostat",
  "Sorafenib", "Irinotecan", "Topotecan", "LBW242", "PD-0325901",
  "PD-0332991", "Paclitaxel", "AZD6244", "PLX4720", "RAF265", "TAE684",
  "TKI258", "Erlotinib"
)

target_list <- c(
  "IGF1R", "ABL", "HSP90", "c-MET", "EGFR", "MDM2", "GS", "HDAC",
  "RTK", "TOP1", "XIAP", "MEK", "CDK4", "TUBB1", "RAF", "ALK", "FGFR"
)
if (FALSE) {
analyze_gene_drug_response_diff("TP53")
analyze_gene_drug_response_diff(c("TP53", "KRAS"), drug = "AEW541")
analyze_gene_drug_response_diff(c("TP53", "KRAS"),
  tissue = "kidney",
  combine = TRUE
)

# Visualization
vis_gene_drug_response_diff("TP53")
}