analyze_gene_drug_response_diff: Analyze Difference of Drug Response (IC50 Value (uM)) between...

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

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

Description

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"
)
## Not run: 
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")

## End(Not run)

UCSCXenaShiny documentation built on March 7, 2023, 7 p.m.