compDrugsen: Comparison of drug sensitivity

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

This function estimates the IC50 of specific drugs for each Subtype by developing a ridge regression predictive model based on all/specific cell lines derived from Genomics of Drug Sensitivity in Cancer (GDSC, https://www.cancerrxgene.org/).

Usage

compDrugsen(
  moic.res = NULL,
  norm.expr = NULL,
  drugs = c("Cisplatin", "Paclitaxel"),
  tissueType = "all",
  test.method = "nonparametric",
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  prefix = NULL,
  seed = 123456,
  fig.path = getwd(),
  width = 5,
  height = 5
)

Arguments

moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
norm.expr	A matrix of normalized expression data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.
drugs	A string vector to indicate the names of the drugs for which you would like to predict sensitivity, one of Erlotinib, Rapamycin, Sunitinib, PHA-665752, MG-132, Paclitaxel, Cyclopamine, AZ628, Sorafenib, VX-680, Imatinib, TAE684, Crizotinib, Saracatinib, S-Trityl-L-cysteine, Z-LLNle-CHO, Dasatinib, GNF-2, CGP-60474, CGP-082996, A-770041, WH-4-023, WZ-1-84, BI-2536, BMS-536924, BMS-509744, CMK, Pyrimethamine, JW-7-52-1, A-443654, GW843682X, MS-275, Parthenolide, KIN001-135, TGX221, Bortezomib, XMD8-85, Roscovitine, Salubrinal, Lapatinib, GSK269962A, Doxorubicin, Etoposide, Gemcitabine, Mitomycin C, Vinorelbine, NSC-87877, Bicalutamide, QS11, CP466722, Midostaurin, CHIR-99021, AP-24534, AZD6482, JNK-9L, PF-562271, HG-6-64-1, JQ1, JQ12, DMOG, FTI-277, OSU-03012, Shikonin, AKT inhibitor VIII, Embelin, FH535, PAC-1, IPA-3, GSK-650394, BAY 61-3606, 5-Fluorouracil, Thapsigargin, Obatoclax Mesylate, BMS-754807, Lisitinib, Bexarotene, Bleomycin, LFM-A13, GW-2580, AUY922, Phenformin, Bryostatin 1, Pazopanib, LAQ824, Epothilone B, GSK1904529A, BMS345541, Tipifarnib, BMS-708163, Ruxolitinib, AS601245, Ispinesib Mesylate, TL-2-105, AT-7519, TAK-715, BX-912, ZSTK474, AS605240, Genentech Cpd 10, GSK1070916, KIN001-102, LY317615, GSK429286A, FMK, QL-XII-47, CAL-101, UNC0638, XL-184, WZ3105, XMD14-99, AC220, CP724714, JW-7-24-1, NPK76-II-72-1, STF-62247, NG-25, TL-1-85, VX-11e, FR-180204, Tubastatin A, Zibotentan, YM155, NSC-207895, VNLG/124, AR-42, CUDC-101, Belinostat, I-BET-762, CAY10603, Linifanib , BIX02189, CH5424802, EKB-569, GSK2126458, KIN001-236, KIN001-244, KIN001-055, KIN001-260, KIN001-266, Masitinib, MP470, MPS-1-IN-1, BHG712, OSI-930, OSI-027, CX-5461, PHA-793887, PI-103, PIK-93, SB52334, TPCA-1, TG101348, Foretinib, Y-39983, YM201636, Tivozanib, GSK690693, SNX-2112, QL-XI-92, XMD13-2, QL-X-138, XMD15-27; two common chemodrugs (i.e., Cisplatin and Paclitaxel) will be analyzed by default if no indication.
tissueType	A string value to specify if you would like to train the models on only a subset of the CGP cell lines (based on the tissue type from which the cell lines originated); Allowed values contain c("all", "aero_digestive_tract", "blood", "bone", "breast", "digestive_system", "lung", "nervous_system", "skin", "urogenital_system") and "all" by default.
test.method	A string value to indicate the method for statistical testing. Allowed values contain c('nonparametric', 'parametric'); nonparametric means two-sample wilcoxon rank sum test for two subtypes and Kruskal-Wallis rank sum test for multiple subtypes; parametric means two-sample t-test when only two subtypes are identified, and anova for multiple subtypes comparison; "nonparametric" by default.
clust.col	A string vector storing colors for annotating each Subtype.
prefix	A string value to indicate the prefix of the output plot.
seed	A integer value to indicate the seed for reproducing ridge regression.
fig.path	A string value to indicate the output path for storing the boxviolin plot.
width	A numeric value to indicate the width of boxviolin plot.
height	A numeric value to indicate the height of boxviolin plot.

Value

Data.frame(s) storing the estimated IC50 of specified drugs per sample within each Subtype.

References

Geeleher P, Cox N, Huang R S. (2014). pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. PLoS One, 9(9):e107468.

Geeleher P, Cox N J, Huang R S. (2014). Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biol, 15(3):1-12.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.