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sens_res_table.R
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sens_res_table.R
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# create table showing resistant/sensitive numbers, thus the need for oversampling
## load necessary packages ----
if (!require ('glmnet')) install.packages('glmnet')
library(glmnet) # for model building
if (!require ('ROSE')) install.packages('ROSE')
library(ROSE)
if (!require('vip')) install.packages('vip')
library(vip)
if (!require('pdp')) install.pacakges('pdp')
library(pdp)
if(!require('patchwork')) install.packages('patchwork')
library(patchwork)
if(!require('pROC')) install.packages('pROC')
library(pROC)
### functions needed ----
# create function opposite of %in%
'%ni%' <- Negate('%in%')
## GDSC ------
# load clinical data ----
bleomycin <- read.csv('Processed_Clinical_Data/bleomycin_gdsc_clinical_processed.csv', row.names = 1)
camptothecin <- read.csv('Processed_Clinical_Data/camptothecin_gdsc_clinical_processed.csv', row.names = 1)
cisplatin <- read.csv('Processed_Clinical_Data/cisplatin_gdsc_clinical_processed.csv', row.names = 1)
cytarabine <- read.csv('Processed_Clinical_Data/cytarabine_gdsc_clinical_processed.csv', row.names = 1)
doxorubicin <- read.csv('Processed_Clinical_Data/doxorubicin_gdsc_clinical_processed.csv', row.names = 1)
etoposide <- read.csv('Processed_Clinical_Data/etoposide_gdsc_clinical_processed.csv', row.names = 1)
gemcitabine <- read.csv('Processed_Clinical_Data/gemcitabine_gdsc_clinical_processed.csv', row.names = 1)
methotrexate <- read.csv('Processed_Clinical_Data/methotrexate_gdsc_clinical_processed.csv', row.names = 1)
mitomycin <- read.csv('Processed_Clinical_Data/mitomycin_gdsc_clinical_processed.csv', row.names = 1)
sn38 <- read.csv('Processed_Clinical_Data/sn38_gdsc_clinical_processed.csv', row.names = 1)
temozolomide <- read.csv('Processed_Clinical_Data/temozolomide_gdsc_clinical_processed.csv', row.names = 1)
#
## load gene expression data ----
gdsc <- read.csv('gdsc_rna_seq_names.csv', stringsAsFactors = FALSE, header = TRUE, row.names = 1)
gdsc_names <- rownames(gdsc)
gdsc <- apply(gdsc, 2, scale)
rownames(gdsc) <- gdsc_names
#
#
#
#
### set up data for model building ----------
# get names of GDSC cell lines treated with each drug
bleomycin_lines <- bleomycin$COSMIC_ID #766
camptothecin_lines <- camptothecin$COSMIC_ID #678
cisplatin_lines <- cisplatin$COSMIC_ID #680
cytarabine_lines <- cytarabine$COSMIC_ID #676
doxorubicin_lines <- doxorubicin$COSMIC_ID #711
etoposide_lines <- etoposide$COSMIC_ID #718
gemcitabine_lines <- gemcitabine$COSMIC_ID #707
methotrexate_lines <- methotrexate$COSMIC_ID # 679
mitomycin_lines <- mitomycin$COSMIC_ID #712
sn38_lines <- sn38$COSMIC_ID #761
temozolomide_lines <- temozolomide$COSMIC_ID #739
bleomycin_rna_seq <- gdsc[rownames(gdsc) %in% bleomycin$COSMIC_ID, ]
bleomycin_rna_seq <- as.data.frame(bleomycin_rna_seq)
bleomycin_rna_seq$res_sens <- bleomycin$res_sens
bleomycin_table <- table(bleomycin_rna_seq$res_sens)
camptothecin_rna_seq <- gdsc[rownames(gdsc) %in% camptothecin$COSMIC_ID, ]
camptothecin_rna_seq <- as.data.frame(camptothecin_rna_seq)
camptothecin_rna_seq$res_sens <- camptothecin$res_sens
camptothecin_table <- table(camptothecin_rna_seq$res_sens)
cisplatin_rna_seq <- gdsc[rownames(gdsc) %in% cisplatin$COSMIC_ID, ]
cisplatin_rna_seq <- as.data.frame(cisplatin_rna_seq)
cisplatin_rna_seq$res_sens <- cisplatin$res_sens
cisplatin_table <- table(cisplatin_rna_seq$res_sens)
cytarabine_rna_seq <- gdsc[rownames(gdsc) %in% cytarabine$COSMIC_ID, ]
cytarabine_rna_seq <- as.data.frame(cytarabine_rna_seq)
cytarabine_rna_seq$res_sens <- cytarabine$res_sens
cytarabine_table <- table(cytarabine_rna_seq$res_sens)
doxorubicin_rna_seq <- gdsc[rownames(gdsc) %in% doxorubicin$COSMIC_ID, ]
doxorubicin_rna_seq <- as.data.frame(doxorubicin_rna_seq)
doxorubicin_rna_seq$res_sens <- doxorubicin$res_sens
doxorubicin_table <- table(doxorubicin_rna_seq$res_sens)
etoposide_rna_seq <- gdsc[rownames(gdsc) %in% etoposide$COSMIC_ID, ]
etoposide_rna_seq <- as.data.frame(etoposide_rna_seq)
etoposide_rna_seq$res_sens <- etoposide$res_sens
etoposide_table <- table(etoposide_rna_seq$res_sens)
gemcitabine_rna_seq <- gdsc[rownames(gdsc) %in% gemcitabine$COSMIC_ID, ]
gemcitabine_rna_seq <- as.data.frame(gemcitabine_rna_seq)
gemcitabine_rna_seq$res_sens <- gemcitabine$res_sens
gemcitabine_table <- table(gemcitabine_rna_seq$res_sens)
methotrexate_rna_seq <- gdsc[rownames(gdsc) %in% methotrexate$COSMIC_ID, ]
methotrexate_rna_seq <- as.data.frame(methotrexate_rna_seq)
methotrexate_rna_seq$res_sens <- methotrexate$res_sens
methotrexate_table <- table(methotrexate_rna_seq$res_sens)
mitomycin_rna_seq <- gdsc[rownames(gdsc) %in% mitomycin$COSMIC_ID, ]
mitomycin_rna_seq <- as.data.frame(mitomycin_rna_seq)
mitomycin_rna_seq$res_sens <- mitomycin$res_sens
mitomycin_table <- table(mitomycin_rna_seq$res_sens)
sn38_rna_seq <- gdsc[rownames(gdsc) %in% sn38$COSMIC_ID, ]
sn38_rna_seq <- as.data.frame(sn38_rna_seq)
sn38_rna_seq$res_sens <- sn38$res_sens
sn38_table <- table(sn38_rna_seq$res_sens)
temozolomide_rna_seq <- gdsc[rownames(gdsc) %in% temozolomide$COSMIC_ID, ]
temozolomide_rna_seq <- as.data.frame(temozolomide_rna_seq)
temozolomide_rna_seq$res_sens <- temozolomide$res_sens
temozolomide_table <- table(temozolomide_rna_seq$res_sens)
sensitivity_thresholds <- c(-1.4805, -6.584, 1.3801, -1.9516, -3.9565, -1.2198, -5.9903, -2.4743, -2.9647, -6.559, 4.6032)
sensitive_samples <- c(bleomycin_table[1], camptothecin_table[1], cisplatin_table[1], cytarabine_table[1], doxorubicin_table[1],
etoposide_table[1], gemcitabine_table[1], methotrexate_table[1], mitomycin_table[1], sn38_table[1],
temozolomide_table[1])
resistant_sampels <- c(bleomycin_table[2], camptothecin_table[2], cisplatin_table[2], cytarabine_table[2], doxorubicin_table[2],
etoposide_table[2], gemcitabine_table[2], methotrexate_table[2], mitomycin_table[2], sn38_table[2],
temozolomide_table[2])
sample_df <- data.frame(sensitivity_thresholds, sensitive_samples, resistant_sampels)
colnames(sample_df) <- c('Sensitivity\nThreshold', 'Sensitive\nSamples', 'Resistant\nSamples')
rownames(sample_df) <- c('Bleomycin', 'Camptothecin', 'Cisplatin', 'Cytarabine', 'Doxorubicin',
'Etoposide', 'Gemcitabine', 'Methotrexate', 'Mitomycin', 'SN38',
'Temozolomide')